Haven't seen the movie yet, but what your saying worries me. Particularly with the "bodies thrown down pyramids" bit, it sounds like they're basing a lot of what is supposed to be the Maya civilization on sixteenth century reports by Spanish conquistadors about Aztec civilization, and that's just too many degrees of separation for me to feel comfortable. And that's probably the reason that you had that feeling of alienization, because honestly, we are so like the Maya that it's rather frightening.

While I'm not going to judge before I see it, it sounds like The Road to El Dorado is closer to the truth than this.