I was into these books along with Helena Blavatasky at one time, I've really scoured the dregs.  

The Gospel of Thomas is the main one and some say that the sayings of the "Jesus" of this book are really the thoughts of the gnostic heretic Valentinus.

It is in the Gospel of Thomas I believe that "Jesus" kisses "Mary Magdalene" openly on the mouth.  That right there would be a good reason to cut it from the Bible; it is a diabolical attack on Jesus' sinless nature.  ( Passionate kissing being a mortal sin ).

The message of these books is, as you might expect, all about love and tolerance, with none of the "You are the children of the devil" or "The unprofitable servants will be cast into the fire" or chasing the money-changers from the Temple.  This "Jesus" comes off as a proto-hippie guru bumming around with a groovy chick ( Mary Magdalene ) and some chill dudes ( the apostles ).  All that's missing are the surfboard and shades.  

Removing one part of Jesus' teachings fits in with what Satan has tried to do throughout history.  The gnostics rejected the fire and brimstone; Calvinists/Protestants reject the mercy.  Both groups turn Jesus into an expression of their own one-track mind and are unable to see Him in His fullness, as both perfect judge and lover of mankind and forgiver of sins.  Most recently the communists tried to paint Him as a proto-communist by emphasizing His rejection of wealth and that most of His apostles were "working-class."  

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The gnostic gospels were "discovered" ( planted? ) in a cave in Egypt somewhere and perhaps were meant to prepare the ground for Da Vinci Code and this whole idea of a lineage stemming from the "child" of Jesus and Mary Magdalene.  Mary Magdalene is central in all these books and is portrayed in a way that suggests she was Our Lord's wife or mate -- whatever your dirty mind chooses -- and that this was somehow denied from the accepted gospels.  If you recall, earlier this century, articles appeared in magazines with Jєωιѕн "experts" saying that Jesus was a rabbi and therefore must have been married.  Well, most rabbis did not wander around preaching outside the temple and getting crucified with thieves.  Jesus was, shall we say, unorthodox, being God and all.

The Gnostic gospels were most likely just a red herring to distract from Vatican II as the idea of the "line of Jesus and Mary Magdalene" never went anywhere.