Christians accept four legitimate Gospels from Matthew, Mark, Luke, and John.
My Question: Did the Catholic Church have evidence to discredit the Gospel of Judas?
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.