This novel is a wild ride. Perhaps its most obvious feature is the inclusion of sexually devious behavior, focusing special attention on the perplexing problems of pedophilia and incest. But these indiscretions are not meaningless—they are both attached to James Piper's difficult past and his inability to adjust to life, a disability that becomes exacerbated by the difficulties of the World War.
James takes a young wife—too young even for her own parents approval—and then Materia develops a suspicion of James that his attraction for her was not an isolated event, and that perhaps, James will develop sexual attractions toward her daughters. Perhaps his attraction is borne from a neglect that he suffered earlier in life. After all, when he took his young wife, he did so out of desperation, without a family to fall back on.
These sexual issues are not the whole of James's issues, and actually James is seen to be something of troubled person in many regards. For instance, it's not clear exactly why he would stop Frances from baptizing the children, just to let one of the babies die in the same scene. How much care was he really taking? This seems like a moment of cognitive dissonance, an account that the reader might question regarding its validity and the trustworthiness of the narrator.
This is ultimately the central thematic aspect of the novel, moralistically speaking: James bears a shame that his family feels as well, because he allowed the difficulties of his life to cause perversion in him that tear the family apart.
