Why the Gospel of Thomas was banned by the church

Why was the Gospel of Thomas banned by the church?

I believe the reason why the church considered the Gospel of Thomas to be anathema was because the story in Matthew that records Jesus as saying to Simon, "You are Peter, and upon this rock I will build my church" is significantly different in Thomas.

Matthew 16:13-17 in the NIV reads:

¹³ When Jesus came to the region of Caesarea Philippi, he asked his disciples, “Who do people say the Son of Man is?”

¹⁴ They replied, “Some say John the Baptist; others say Elijah; and still others, Jeremiah or one of the prophets.”

¹⁵ “But what about you?” he asked. “Who do you say I am?”

¹⁶ Simon Peter answered, “You are the Messiah, the Son of the living God.”

¹⁷ Jesus replied, “Blessed are you, Simon son of Jonah, for this was not revealed to you by flesh and blood, but by my Father in heaven. ¹⁸ And I tell you that you are Peter, and on this rock I will build my church, and the gates of Hades will not overcome it.

The parallel passage in Thomas (logion 13, Lambdin translation) reads:

Jesus said to his disciples, "Compare me to someone and tell me whom I am like." 
Simon Peter said to him, "You are like a righteous angel." 
Matthew said to him, "You are like a wise philosopher." 
Thomas said to him, "Master, my mouth is wholly incapable of saying whom you are like." 
Jesus said, "I am not your master. Because you have drunk, you have become intoxicated from the bubbling spring which I have measured out." 
And he took him and withdrew and told him three things. When Thomas returned to his companions, they asked him, "What did Jesus say to you?" 
Thomas said to them, "If I tell you one of the things which he told me, you will pick up stones and throw them at me; a fire will come out of the stones and burn you up."

The two accounts clearly retell the same incident, but the differences are striking. In the Matthew passage, Jesus renames Simon as Peter. The early church, based in Rome, developed its idea of being authoritative from this passage. According to tradition, Peter was the first Pope, and all popes since then have been the spiritual heirs of Peter. In the Thomas passage, Jesus denies Messiahship, saying instead that the Father has empowered Thomas to be his twin. 

There are many things we can say about the words used here. Firstly, Jesus was of course a Jew and not a Christian, but Matthew has Jesus using the word 'church'--surely an anachronism? And secondly, the name 'Peter' in Greek means 'rock'. For me, this is a cleverly written and structured piece of persuasive writing.

So too is the Thomas passage, for the name 'Thomas' means 'twin', and we will dream forever about "the things that he told me", what they might have been...

However, the reason the church wanted this gospel destroyed is, I believe, simply because its existence removes the papacy's claim to being the Christian movement's legitimate authority.