Did the Catholic Church have evidence to discredit the Gospel of Judas?

Your question assumes that the (Roman) Catholic Church set the canon of the New Testament. This is not true.

The See of Rome - which following a schism with the east came to be known as the "Roman Catholic Church" - played a relatively minor role in setting the New Testament canon. The local council of Carthage (in modern day Tunisia) - a city that at that time fell under the See of Rome - did set a canon for that particular region in 397, but the council basically confirmed the canon that had been already used in the east. This canon had been affirmed previously by Athanasius of Alexandria (ca 296-373), bishop within the See of Alexandria, in what has been come to be known his "39th Letter". The final and formal setting of the New (and Old) Testament Church for the entire Church - i.e. the Sees of Rome, Constantinople, Alexandria, Antioch, and Jerusalem - took place at the 7th Ecumenical Council at Nicea in 787.

The Concise Oxford Dictionary (11th ed.) defines "discredit" as to "harm the good reputation of". Your question presumes that the Gospel of Judas had some good reputation among the Church Fathers to harm to begin with. This appears not to have been the case.

The early Church Father Irenaeus of Lyon (130-202) wrote of the Gospel of Judas:

Others again declare that Cain derived his being from the Power above, and acknowledge that Esau, Korah, the Sodomites, and all such persons, are related to themselves. On this account, they add, they have been assailed by the Creator, yet no one of them has suffered injury. For Sophia was in the habit of carrying off that which belonged to her from them to herself. They declare that Judas the traitor was thoroughly acquainted with these things, and that he alone, knowing the truth as no others did, accomplished the mystery of the betrayal; by him all things, both earthly and heavenly, were thus thrown into confusion. They produce a fictitious history of this kind, which they style the Gospel of Judas.¹

The Gospel of Judas emerged - probably in the 2nd century - out of some gnostic sect. Gnosticism is largely founded on an idea of creating higher religious/philosophical knowledge (gnosis) by uniting Greek philosophy with elements of eastern religions like Zoroasterianism.²

Gnosticism was condemned even during Apostolic times. Simon Magus (Acts 8:9) is considered a kind of proto-Gnostic. Other early gnostics condemned in the Apostolic writings were the followers of Cerinthus the Alexandrian, the Docetists (condemned in 1 John 4:2-3), and the Nicolaitans (Revelation 2:5-16).

<sup>1. Against Heresies, I.XXXI.1
2. See, e.g., Orthodox Dogmatic Theology (3rd ed.; St. Herman of Alaska Press, p.375ff)</sup>

This question is based on a faulty premise - namely that any individual "suppressed" any book in the canonization process. To say that a book was "discredited" or "suppressed" from the canon is akin to saying that "Fifty Shades of Grey" was "discredited" from the NY Times Best Seller List, or that the kid with an SAT in the 80th percentile was 'suppressed' from attending Harvard.

Canonization was a selective process in which the most widely circulated books and most widely quoted books were endorsed by Christian scholars. Anything less wasn't "evil" - it just wasn't as good. There were literally hundreds of books authored in the first four centuries that called themselves "Gospels." From the Gospel of Thomas to the Gospel of Peter to the Gospel of the Hebrews to Marcion's Gospel, there were all sorts of "Gospels" to choose from. Only those that were "most profitable" gained the widest circulation, eventually, over many centuries (Athanasius' Festal Letter in 357 is the earliest complete list!) were viewed as authoritative.

In the case of the Gospel of Judas, its just not very good. It's a Gnostic Gospel which concentrates on proving the evilness of matter and thus claiming that Jesus himself was a docetic God - he only appeared to be a man. Contemporary "Mainstream" Christianity from Paul's time onwards rejected that notion, and therefore didn't follow it.

THe Gnostics went their way and the Christians went theirs. The Gnostics lost and the "Catholics" (i.e. the rest of the "Universal" church) felt no need to preserve something they didn't find useful. End of Story.