Native American imagery
The use of Native American religion draws a sharp contrast to the European settlers'. The religion of the natives is primal and ground-up. In other words, they start with their true emotions about a situation and understand themselves in light of natural systems and orders. That isn't like the Europeans at all, because the Europeans start with ideas and then make their bodies obey those constructs. Native Americans start with their bodies and submit their bodies to their instincts; that is the difference depicted in the novel.
Sacrifice and death
Both stories share strong uses of sacrifice. The Natives attempt to sacrifice Everell as a blood atonement for the wrongful death of one of their own, but Magawisca sacrifices her own reputation and fate to save Everell. One use of sacrifice depicts justice, the other depicts mercy. How different is that than the Christian opinion? It is not different, as the story shows. Alice sacrifices her life in a round-about way, and William sacrifices to raise her children in her wake. Parenthood is shown as a sacrifice.
The occult
The use of witchcraft, elemental magic, and herbal cocktails add a flavor to the book that speaks of the sublime order behind the veil of reality. This is the sublime realm that the Christian myth refers to as well (in fact the Bible makes very frequent mention of such magic), but the Christians are not allowed by their religion to practice such witchcraft, so the use of the occult reminds them of hellish themes, adding a horrific, confusing tone. This confusion underlines the differences between the cultures.
Social construct
The novel starts right away with a heart-breaking use of abstract imagery. Although the physical and emotional imagery of William and Alice's romance is obvious, even archetypal, the religious social constructs that govern their community come between them. Alice is forced to marry someone she doesn't love, because they profess different beliefs. Never mind that their love for one another is part of their shared religious experience—the father says social constructs must be obeyed, regardless.