The reader isn't shown the good side of the church and it does far too much evil. I don't really mind the relative evil or good of the church, I just don't buy that something that is that blatant with as many information leaks as it potentially has (because of escaping witches and what not) would be able to possess that level of overt power. Especially since every witch is ultimately someone's daughter, and there are several who still accept their child as their child after she becomes a witch.. I'm not saying that they need to be any less evil (they're after all motivated by the most evil of phrases, "The ends justify the means") just that the reader should be shown a little more of why the faithful are so faithful. Standing up against monsters is not enough, after all, humans are too greedy to see such a thing as a benefit when it is actually happening far off. At least, in the long run. Plus, with all the starvation and what not it can hardly be said that the church is doing enough to overcome what should be seen as strong negatives and suspicious behaviors, such as the existence of the various pills and a superhuman army.