Could the thorn that was given to Paul be a mortal sin?

No, it could not be a mortal sin. If you read on to the commentary paragraph 477, even St. Thomas seems to attribute the thorn to either a bodily weakness or a concupiscence:

477. – He says therefore, I asked, but the Lord said to me, my grace is sufficient for you. As if to say: it is not necessary that this bodily weakness leave you, because it is not dangerous, for you will not be led into impatience, since my grace strengthens you; or that this weakness of concupiscence depart, because it will not lead you to sin, for my grace will protect you: “Justified by his grace as a gift” (Rom. 3:24). And of course, God’s grace is sufficient for avoiding evil, doing good, and attaining to eternal life: “By the grace of God I am what I am” (1 Cor. 15:10); “But the free gift of God is eternal life in Christ Jesus our Lord” (Rom. 6:25).

Several modern commentaries such as the ESV Study Bible has this to say on the thorn (2 Cor 12:7):

12:7 a thorn was given me (by God, who is sovereign over all things) in the flesh, a messenger of Satan. The nature of this “thorn” or “messenger” is much disputed. The most frequently proposed possibilities include: (1) Paul’s inner psychological struggles (such as grief over his earlier persecution of the church, or sorrow over Israel’s unbelief, or continuing temptations); (2) Paul’s opponents, who continued to persecute him (cf. Num. 33:55 and Ezek. 28:24, where thorns refer to Israel’s enemies); (3) some kind of physical affliction (possibly poor eyesight, malaria fever, or severe migraine headaches); or (4) some kind of demonic harassment (“a messenger of Satan”). Most commentators cautiously prefer some form of the third view, since “thorn in the flesh” would seem to suggest a physical condition.

Another commentary Augsburg Commentary by Frederick Danker on 2 Cor 12:5-7 has a similar conclusion to say (physical disability or deficiency) making its argument based on the Greek rhetorical technique that Paul must have used in writing his letter.

5-7: If Paul were to boast about his visions, he could himself become the center of a personality cult. But the truth of the gospel would be up for grabs; for each claimant of special revelation could put in a pitch for the loyalties of God’s people. Paul refuses to take that route and prefers to boast only about his weaknesses, for through Paul’s weaknesses the divine strength is displayed. With this statement he indicates, of course, that he disavows the validity of all his boasting that was done in irony in the paragraphs that preceded. The Corinthians could not fail to grasp the implications for their own assessment of the apostle. Any charges of lack of theological sophistication do not hold up. Paul could sound very esoteric, if he wished, but it would not be to the Corinthians’ best interests.

Most of the Corinthians would by now be applauding Paul’s cascading oratorical brilliancies. By maintaining the charade of talking about a person other than himself, Paul facetiously suggests that he avoids the distaste attached to self-praise. In his essay On Inoffensive Self-Praise (542e), Plutarch states that “people who feel compelled to engage in self-praise will make it easier for themselves if they do not attribute everything to themselves but shift the burden of glory to fortune or to God.

Four centuries earlier, Demosthenes had modeled the thought. In the middle of one of his self-evaluations as defender of the interests of Athens, Demosthenes says that he could say much more, but is cautious about arousing resentment because of his apparent boasting (259). People who receive favors ought to be honorable enough to express appreciation, he says, “but one who has conferred them ought to forget them immediately.” Hence, he goes on to say, “I will not be inveigled into saying any more about them. The respect I have already reaped because of them suffices” (269). It is a line of thought rooted in the Delphic maxim, “Know yourself.”

Paul knows the rhetorical code and states that he is worried lest the very abundance of the revelations should lead to any one’s overestimation of the apostle. The opening clause of v. 7 in the Greek text consists of the words, kai tȩ̄ hyperbolȩ̄ tōn apokalypseōn (“and because of the abundance of revelations”). This phrase has caused difficulty because of uncertainty about its grammatical connection. The RSV construes it with the words that follow, but stylistic and textual-critical considerations weigh against such interpretation. At the same time, those who construe the phrase with the preceding verse encounter difficulty in the conjunction dio (which is ignored, apparently for textual-critical reasons, by the RSV). The problem is best resolved along the following lines. (1) The phrase is to be taken with v. 6, and is to be rendered: “(than he sees and hears from me), especially (kai) because of the abundance of revelations.” (2) The connection between this phrase and the succeeding clauses is expressed colloquially. The apostle’s thought leaps ahead of his grammar. Abundance suggests hazard, and consideration of hazard requires a transition that involves use of a causal conjunction; hence the choice of dio (“therefore”). Verse 7 should, then, be rendered: “(than he sees or hears from me), especially because of the abundance of revelations. Therefore, to keep me from being too elated, a thorn was given me in the flesh.…”

With the keen sense of humor that prompts comedians to make themselves butts of their own jokes, Paul says that in the face of an array of revelations he received an antidote. The apostle maintains the strain of folly that runs through the entire autobiographical speech by characterizing the antidote as a benefaction (edothē, was given). The logical grammatical donor is Satan, for the donation of the thorn is defined as Satan’s messenger. But it is generally understood by biblical writers that Satan performs his functions within the boundaries of divine permission. The humor in Paul’s reference to Satan lies in the fact that Satan, who is known in Jewish tradition as God’s arch-rival, with a colossal ego, would cross the rhetorical stage as a competitor who sends Paul an antidote to possible pride and arrogance. Since God is ultimately responsible, the humor is doubly sharp. In the sophisticated rhetorical context of the “Fool’s Speech,” an anecdote like this communicates with several circuits open.

Just as second-century Christian storytellers loved to fill in biographical holes left in the Gospels and Epistles, so commentators have filled the literature of interpretation with a long list of equations, ranging from epilepsy to competitive congregational leaders, for Paul’s delightfully inscrutable “thorn.” But its identity, like that of various ritual acts in antiquity, will be an eternal mystery. Certain it is that the “thorn” was a source of pain and humiliation for the apostle, and more probably a physical disability or deficiency than hostility from human opponents. In any case, the lesson for the church is obvious—evaluation of service, when otherwise well rendered, is not to be contaminated by consideration of physical disabilities.

Finally, the IVP Dictionary of Paul and His Letters in section 2 (Illness As a Messenger from Satan) of the entry on HEALING, ILLNESS (by Graham Twelftree, Ph.D.) has this to say specifically covering 2 Cor 12:7, reaching similar conclusion (illness or a range of physical disorder) after an extensive historical survey of famous commentators:

In 2 Corinthians 12:7 Paul says that in order to keep him from being too elated by the abundance of revelations (see Visions), a thorn in the flesh, a messenger of Satan, was given him to batter him. The nature of this thorn (skolops) has been much debated. As early as Chrysostom (On Second Corinthians 26.2) the view was propounded that the thorn is to be understood as the persecution Paul experienced, including that from his enemies at Corinth. For, the thorn is characterized as an “messenger” or “angel” (angelos, 2 Cor 12:7) of Satan, implying a person or group (cf. Satan as “angel of light,” 2 Cor 11:14), and “to batter” (kolaphizō, 2 Cor 12:7) is a personal activity. Further, the context of the passage is Paul’s struggle with his opponents (2 Cor 10–13) and Numbers 33:55 (LXX) uses the image of a thorn for the enemies of the Israelites. However, on the other hand, the thorn may have been given to Paul near the time of his visions and revelations when he had yet to confront his opponents. Also, the reference to a messenger or angel of Satan does not seem like a reference to a group of opponents, and in 2 Corinthians 11:14–15 his opponents are Satan in disguise as his servants (diakonoi) rather than his messengers.

A view from the Middle Ages is that the thorn is every kind of temptation (cf. Calvin Commentary), or sexual temptation in particular. But this does not accord with the list of hardships and weaknesses (see Affliction, Trials, Hardships) in 2 Corinthians 11:23–29 and 12:10, and it requires too narrow a view of “flesh.” Also, 1 Corinthians 7:7 implies that Paul did not struggle with sexual temptation (see Sexuality).

The majority of interpreters, from Tertullian onward (Pud. 13), take the thorn to be some form of physical illness. In favor of this view is the metaphor of a thorn, the connection in ancient times between demonic manifestations and physical illness, and the structure of the 2 Corinthians 12:7–10 passage imitating the narratives of a healing miracle.

Due to the scarcity of data, some scholars do not attempt a diagnosis of the illness. Others have suggested epilepsy (as a result of Paul’s conversion experience; see Conversion and Call), hysteria, migraine, depression, severe sciatica, rheumatism, poor hearing, leprosy, stammering and solar retinitis (an inflammation of the retina caused by the blinding light at his conversion). Lightfoot used Galatians 4:13, 14 (see 3 below) to interpret the meaning of the thorn as an ophthalmic complaint. Ramsay’s view, that Paul contracted recurring malarial fever in Pamphilia, is often accepted since it takes account of the thorn as being a physical disorder, one that is felt continually or often as battering (2 Cor 12:7, kolaphizē, present tense), and humiliating while not stopping Paul’s rigorous mission work.

In so far as Paul intended the thorn in the flesh to denote a physical ailment (with sarx, “flesh,” taken to refer to the physical body; see Flesh), he expresses a number of his views on illness and healing in this passage. First, the illness humbled Paul, preventing him from becoming conceited. Second, this illness is a messenger from Satan causing pain and humiliation. Yet, third, the use of the passive edothē (“was given,” 2 Cor 12:7) is a veiled allusion to the illness being given by God. Paul resolves this paradox by saying that the Lord’s grace is shown to be sufficient for him even though his three requests for the thorn to leave him were not answered as he expected. Thus, fourth, Paul does not view illness as something the Lord always heals, though remaining weakness makes the power of Christ more evident in his life to the point of Paul boasting in his weaknesses (2 Cor 12:9–10).

Question: Could the thorn that was given to Paul be a mortal sin?

To understand this within the biblical context, it helps to define a few things.

In the Catholic Church, a mortal sin is defined here in this way.

1857 For a sin to be mortal, three conditions must together be met: "Mortal sin is sin whose object is grave matter and which is also committed with full knowledge and deliberate consent."

1858 Grave matter is specified by the Ten Commandments, ...

1859 Mortal sin requires full knowledge and complete consent. It presupposes knowledge of the sinful character of the act, of its opposition to God's law. It also implies a consent sufficiently deliberate to be a personal choice.

Did Paul commit a Catholic's mortal sin? Here is Paul on the thorn.

And lest I should be exalted above measure through the abundance of the revelations, there was given to me a thorn in the flesh, the messenger of Satan to buffet me, lest I should be exalted above measure. 2 Cor 12:7

The thorn, leaving aside the question of what that was, was given to Paul. It wasn't an action by Paul. So it fails their third requirement. Paul did not choose it, did not consent to it. In fact, Paul asked three times for it to be removed.

For this thing I besought the Lord thrice, that it might depart from me. v8

Paul continues.

Therefore I take pleasure in infirmities, in reproaches, in necessities, in persecutions, in distresses for Christ's sake: for when I am weak, then am I strong. 2 Cor 12:10

Sicknesses, insults, persecutioins, distresses for Christ's sake certainly are not part of the 10 Commandments. So now we find that Paul fails their first test of their mortal sin idea. Paul was not committing grave matters.

The third test is similar to the second test. While Paul had full knowledge of the thorn, the context of this requirement is that the matter includes a breaking of Law, of consenting fully to breaking the Law. As with the other two parts of the definition, Paul is not a suspect. To clarify this comment, having full knowledge of something, by itself, is not a sin, not a problem. Full knowledge in the Catholic theology about mortal sin means one knows something is a sin. The 10 commandments are fully known by Christians. The full knowledge issue for Catholicism arises when one knows a commandment (a grave matter), yet chooses with full knowledge and full consent to transgress anyway.

In conlusion, the thorn in Paul's flesh was not a Catholic's mortal sin. It fails all three of their definitional tests.

As a Protestant, let me offer a different interpretation: the phrase "thorn in the flesh" should not be taken in isolation - it has meaning in an Old Testament context. In Numbers 33:55 the Israelites were warned concerning the heathen Canaanites: But if you do not drive out the inhabitants of the land, those you allow to remain will become barbs in your eyes and thorns in your sides. They will give you trouble in the land where you will live.

Secondly, Paul goes on to clarify: the "thorn" was a messenger of Satan. In other words, it was an evil spirit. Exactly how it afflicted him is not explained, though the idea that it stirred up the persecutions Paul suffered is one interpretation.