It is true that there is an overly violent tribe, but they are balanced out by a peaceful tribe.
I think specifically of the scene early on when Jaguar Paw's tribe is met by another tribe. Frightened, and a bit creepy in their own right, this third tribe is allowed free passage by Jaguar Paw's tribe.
The main dramatic thrust of the piece comes from the difference in ideology of the two main tribes, which is also born out in the characterization and set design each group is given.

I agree wholeheartedly on this standing outside America's usual racial conversation - had this been set in Africa during the same time period I can imagine tons of uproar. Hell, I don't even know if a film version of "Things Fall Apart" could be made because of the many cultural elements Achibe gave to the story that would be shouted down on a public release. (Why are they all dancing around a fire? Why are these people wearing masks, the villagers have to know they aren't gods!)

I watched "Braveheart" tonight and couldn't help bring myself back to this conversation. When it was over my lady and I went online and found a slew on factual inaccuracies, and the homo- and Anglophobic elements were in full force.
I think at the end of the day we can make a few assessments on Mel Gibson the film maker:
He makes entertaining, engaging films from a fresh perspective.
He likes violence. A lot.
He has lots of inner demons that work themselves into his films.
He thinks about religion with a deep zealotry that he then gives to all of his characters. This does not mean it always manifests in the characters as religious devotion, but the majority of his characters are driven by an unwavering belief in something.
To paraphrase one of my favorite teachers, he cares more about "Truth" than he does about "truth," and it is this desire to get to the heart of a story that gets him into hot water.


EDIT: And since I forgot to mention it above... if as you say there was little to no conflict amongst the Maya at the time this movie takes place that is a pretty big leap and does reinforce a myth which screams laziness. If you want it in that time and place, why not move it north a bit and put it with the Aztec? And they shot in Mexico? Cmon, Mel.