John lacks this Jewish trial scene entirely.
John's Gospel does indeed include the trial before the Sanhedrin. The difference is that in John, Jesus first goes to the former High Priest Annas before He is taken to Joseph Caiphas. It is in John's Gospel that the servant of the High Priest slaps Jesus in the face. To say that there is no trial in John shows me that the lady who wrote that hit piece on Mel hasn't picked up the NT in a long time.
As far as the other criticisms, none of the Gospels contradict each other on Jesus' last words. It's always been traditional that He said "Eli Eli...", then His last cry was "It is Accomplished!" before commending His noble spirit to His Father in Heaven. This is complete nitpicking on the authors part; every other film on Jesus has used the last words of Christ in the traditional form, and I've never heard about any scholars objecting then. Attacking Mel on this point is attacking the whole of Christian tradition.
As for the nuns writings, Anne Catherine Emmerich is about to be beatified by the Catholic Church and her writings are fully in line with the mystical writings of other saints and holy people. Great artists from the Middle Ages and the Rennaissance period often used the saints descriptions of Christ and the Blessed Mother in their works(for instance, probably the most famous crucifixion painting, by Matthias Gruenwald, was inspired by the visions of St. Bridget of Sweden). Why shouldn't Mel be allowed this bit of artistic freedom and license?
Certainly the same people who are now attacking Gibson for making this film didn't seem to mind when Scorcese used a 1944 novel by an excommunicated Greek Orthodox laymen for inspiration for his film about the death of Christ.