The story juxtaposes a moral culture of life against a moral culture of death. In Catholic theology, Mary is the mother of the body of Christ. In the story Jaguar Paw and his trib are the culture of life and would represent her children...before they were born. The Aztec/Mayans (IMO calling them Mayans is a brilliant move) would represent the other side, those who have given in to Satanic forces. Therefore this is a battle between the woman and her (preborn) offspring and the serpent and his (Gen 3:15- 1st reading on the feast day) .
Unlike others I think Gibson took ethnic culture off the table completely by making every character in the story "Mayan". I saw nothing taking a position about Western Civ.
The structure of the story seems chaiastic; revolving around a prayer from a desperate woman to a tender spirit mother for the sake of her children. This is a prayer that to any believing Catholic can only be answered by one woman.
“Holy Mother of God and of the Church, our Lady of Guadalupe, you were chosen by the Father for the Son through the Holy Spirit. You are the Woman clothed with the sun who labors to give birth to Christ while Satan, the Red Dragon, waits to voraciously devour your child.” http://www.sancta.org/patr-unb.html) Go to that website and look at the images and compare them to the images of Apocalypto and I think you'll start to see the worldview being expressed. .
(note - Our Lady of Guadalupe, the Marian apparition of Juan Diego, is Patroness of the America's and also of the unborn)
I should have mentioned that the Feast of the Immaculate Conception is a Marian feast day and in Catholic theology references to Eve also apply to Mary who is considered the "new Eve".