Why does John 1 say "the Word was with God" and not "scripture was with God"?

The answer depends on what “the Word” in John 1:1 means.

Ordinary Meaning

Logos is a standard Greek word and means “the expression of thought … as embodying a conception or idea” (Vine's Expository Dictionary).

Greek Philosophy

However, in Greek philosophy, Logos had a very special technical meaning. The first philosopher to use this term was Heraclitus (c. 535 – c. 475 BC) (F. E. Peters, Greek Philosophical Terms, New York University Press, 1967.). He used the term for the divine principle of order and reason in the cosmos. (Christianity.com OR Cambridge Dictionary of Philosophy (2nd ed): Heraclitus, 1999.)

It is possible that Logos in John 1:1 has the meaning that the word logos has in Greek philosophy because Harris claims that John adapted Philo's concept of the Logos, identifying Jesus as an incarnation of the divine Logos that formed the universe. (Harris, Stephen L., Understanding the Bible. Palo Alto: Mayfield. 1985. "John" pp. 302–310) Philo of Alexandria (AD 20-50) was a Hellenistic Jewish philosopher. He attempted to harmonize Jewish scripture with Greek philosophy by combining Plato and Moses into one philosophical system. (Moore, Edward. June 28, 2005. "Middle Platonism – Philo of Alexandria")

God’s Redemption Plan

Some Christians propose that John used Logos in another special sense, namely for God’s plan for the redemption of sinners. In this interpretation, the Word was “in the beginning with God” in the sense that this always was God’s plan. And "The Word became flesh" (John 1:14) in the sense that, when Christ was born, God’s eternal plan was implemented in Christ. The websites Christadelphians, Bibleanswerstand, and The Bible Concealed explain this view. This view is primarily justified by comparing John 1:1-5 to the introductions to some other gospels and letters (1 John 1:4, Mark 1:1-5, Luke 1:1-4, and Titus 1:1-3). These introductions also contain the words and concepts “beginning” and “logos” but, in these instances, it is argued, the beginning is the beginning of Christ’s ministry and does not refer to the creation of “all things.”

The Eternal Son of God

The traditional interpretation of John 1:1 is that John is here using Logos not in any of the senses above but in another special sense, namely of the pre-existent Jesus Christ.

Conclusion

So, as far as I am aware, there are four possible different meanings of the logos in John 1:1.

1. The general sense of “the expression of thought;”
2. The special sense in Greek philosophy of “the divine principle of order and reason in the cosmos;”
3. A somewhat special sense for God’s eternal plan of redemption; and
4. In another special sense for the eternal Son of God.

Your question is, Why does John 1 say "the Word was with God" and not "scripture was with God"? I assume that you ask the question because the Bible often refers to the Scriptures as “the Word of God.”

“Scripture” might arguably be a suitable translation:

If John 1:1 uses logos in the general sense of “the expression of thought,” and if we understand John 1:1 to use this term as God’s “expression of thought,” or

If John 1:1 uses logos for God’s eternal plan of redemption.

But if John 1:1 uses logos in the special sense in Greek philosophy of “the divine principle of order and reason in the cosmos,” or to refer to the eternal Son of God, “scripture” will not be appropriate.

Why John used the word Logos (λόγος) is open to debate, but I think that there are two main reasons.

First, using logos ties back to the thought of the philosopher Philo, thus providing a transition into the gospel and the nature of Christ. Philo was a Jew who lived in Alexandria and whom the Stoic philosophers there influenced. He thought that God's perfection did not allow Him to have any direct contact with the world, so that He had to have a mediator. Philo believed that this mediator took the form of an inferior god, the Logos, who was the link between God and man. By using the word Logos in John 1:1, John indicated that Jesus is the sought-for Mediator. By declaring that the Word was with God and was God, John transitioned into the true nature of Christ by showing that Jesus was not the same as Philo's conception of the Logos.

Second, saying that Scripture was with God and was God in the beginning is not what John was trying to convey, and is therefore insubstantial. John is the only writer in the New Testament to use Logos in such a fashion, and he does so in four places: John 1:1, John 1:14, 1 John 5:7, and Revelation 19:13. These verses indicate that Christ is the Logos, not Scripture itself. Using the word Scripture in John 1:1 obligates one to use "Scripture" in 1 John 5:7, thus "...the Father, the Scripture, and the Holy Spirit; and these three are one." and also in Revelation 19:13, thus that He who judges, makes war, whose eyes are a flame of fire, and who has many crowns, must also have the name "Scripture". Rather this Person is the Logos, the Mediator between God and man and God Himself. Note that Hebrews says that there is one Mediator between God and man: the man Jesus Christ.

Note also that John was written for the Greeks as well as the Jews, for John explains many Jewish words and concepts.

My sources are the several excerpts from Bible scholars including Marvin R. Vincent, Hugh R. Mackintosh, and Frederic Godet contained in the website http://www.bible-researcher.com/logos.html, as well as the Bible study on the book of John titled "Be Alive" by Warren W. Wiersbe.

In a sense, this is a metaphor for Jesus. In the beginning was the word (Jesus) the word was with God (Jesus with God) and the word was God (Jesus being a part of the "Godhead" trinity). Word here in my opinion, does not reflect upon scripture itself, but it represents Jesus. Thus Jesus became flesh and dwelt among us.

There is no need to interchange words in this case, the verse stands on its own. It doesn't say scripture was with God because it was nothing that was written, the Word is an actual being. The Word was with God and the Word was God. The Word is Jesus Christ And the Word was God. The word God identifies the name of a "family", the same as Human beings identify a "family". Birds identify a "family", dogs and cats identify a "family" So it would make sense that if Jesus is of the "family" of God he would be called God. The same that our children are called human. We have different names, personalities, beliefs but we are members of the Human family, the same as Jesus is of the God family. Although he has a different name he's identified as God because he is of the God family. Make sense?

It's because the Greek word translated as "Word" is "Logos" and it basically means" something that communicates." Historically, it has a very particular philosophical meaning that may encompass "Scripture," but also exceeds it.

The Context of John 1:1 and John 1:14 speaks of a Person having the function of being the Logos in the sense of "revealer":

John 1:18 No one has ever seen God yet; The Unique One [who is] God [in nature], is in the bosom of the Father. This one he did exegete.

In the beginning was the Word, and the Word was with God, and the Word was God. (John 1:1, NIV)

All Scripture is God-breathed and is useful for teaching, rebuking, correcting and training in righteousness. (2 Timothy 3:16, NIV)

The Greek word for 'Word' in John 1:1 is Logos(λόγος) and 'Scripture' in 2 Timothy 3:16 is Graphey(γραφή). Though 'Word' and 'Scripture' are very much related, they are necessarily not the same.

The 'Word' in the context of John-1 is a divine entity, which is Jesus Christ, who existed in the beginning with God. 'Scripture' in the context of the Bible mostly refers to the written words of God. Scripture is a subset of the Word. The Scripture may represent the Word and illustrates the picture of the Word but it cannot fully explain it, because scriptures are written in human language which has limitations to describe Heavenly things.

We cannot say that the words we have in the Bible are the only words that God has spoken. Therefore, the Scripture that we have is not equivalent to the Word, it is only part of the Word. Hence, John 1:1 was written as such by the writer, using Word(λόγος), instead of Scripture(γραφή), where the Word refers to Jesus Christ, who is the source of Scripture.