I think the point that was made about scripture holding more weight than someones opinion of history was a good one, and in the context of the trinity, the fact that it is taught in scripture would not be changed even if there were some missing books.
The gospel of Thomas is an obvious forgery made by gnostics and had no relation to scripture. If you read it, you will see just how silly and reprehensible it is. If it were actually written by Thomas, you'd think that the churches he established on the Malabar coast of India would have had some similarities to it's teachings.
Typically, people who say that the early church excluded parts of the bible, and then point to gnostic texts as examples have no concept of Church history or Christian theology. Canonization of the books of the bible was a mere recognition of what Christian churches had already accepted and were already using. Look at the writings of the early church fathers, students and friends of the apostles picked by Jesus, and students of those students, etc. They quote the Bible quite frequently, but they don't promote the gnosticism found in those non-biblical gnostic texts. You can just about recreate the new testament from early patristic quotations, and the new testament itself is completely at odds with gnosticism.
There is no Q. Q is an imaginary hypothetical concept with no manuscripts to verify it's existence.