How do you imagine "churches rejected" the Gospel of Thomas? Because Origen cited it as a real record of Jesus. He was the pre-eminent scholar of early Christianity, btw.

The date of authorship for the GoT is not known, and you grossly exaggerate the available facts on that question.

The reality is that early Christians were probably just mystified by it, and were inclined to trash anything that presented interpretive challenges.

I studied the issue of early Christians demanding comprehensibility from the New Testament here:

https://medium.com/belover/what-cuts-did-christianity-make-to-the-bible-2af8cf351edd