Consider the problem of human religion. There is an assumption made by the Catholic missionaries in this book that the religion they received from their religious tradition is essentially different in intent and execution than the religions that already existed in Native American life. In other words, why did they treat new religious ideas as if they were inferior to the Europeans' own? Couldn't it have been different, hypothetically? One might imagine an exchange of ideas between two peoples who do not automatically suppose "They're wrong and we're right."
The beauty and balance of life and of the social fabric of Native life is offered as an argument that those Catholics missed an opportunity not to teach "savages" about God, but to understand that without the strictures of European progress and society, those "savages" are literally demonstrating the order of the universe, unfettered by the ideas of Greco-Roman tradition. That doesn't mean that anyone is wrong or right, and those points of view can both be understood in helpful ways or harmful ways, so the novel encourages the reader to resist the temptation to indulge in contempt prior to investigation.
Why should the reader bring so much theology into their analysis of the novel? Because other characters demonstrate that very thing by invoking God in the details of their daily lives. The characters talk about "What God wants" for their love lives, but ultimately, this is problematic, because characters like Pauline might begin to use their beliefs about God to harm themselves, and she does literally begin to harm herself in the name of God. This is obviously suggesting that the reader take another critical look at their relationship to religion.
