I think that principally, Mel Gibson makes the Mayans appear unsophisticated and essentially brutish and evil. I suspect that as a member of an extreme branch of Catholicism, Gibson's intentions are always going to be under scrutiny. It could be suggested that he portrayed the Mayans in this way, because he firmly believes that they were evil and therefore the Spanish Conquest was a triumph over evil!
Anyway, Mayan culture faded away around 900 AD and I think it's the Incas that are supposedly portayed in the film, who I might be correct in thinking weren't that big on human sacrifice, unlike the Aztecs in Mexico, who were. You've got to bear in mind though that the destruction of the Aztecs was brought about because of the siliarities their religion had with Catholicism. The Catholics had no problem with other religions, but aspects of the Aztec religion seemed to them a parody of Christianity, and therfore a heresy. So, they had to die!