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.
- The general sense of “the expression of thought;”
- The special sense in Greek philosophy of “the divine principle of order and reason in the cosmos;”
- A somewhat special sense for God’s eternal plan of redemption; and
- 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.