The monk might be doing some questionable things, but he's so badass and Sugita that I can't hate him.
So far there seems to be two possibilities for how this society came about. The first is that the scientists are indeed still in charge, and Saki's flashbacks are meant to serve as proofs of their presence. All the religion stuff is merely a front to make the people easier to control and less likely to question. We'll probably see the masterminds sooner or later.
Or it can be that the system had become so automated by a few decades after the Dark Age that the scientists have lost their science. When they can no longer understand their own devices, they think of it as magic. The rituals and rules left now are merely relics perpetuated by custom. There are no masterminds, but a society stuck in the past.