The Seers aren't supernaturally evil, not in the way people think they are. The point of them is that they're oh-so-very human antagonists. Everything they seek to achieve, they do in the name of the same sort of self-advancement we all indulge in. A Seer wants job security, the confidence that tomorrow won't present challenges she's not ready for, the ability to achieve the kind of life she wants for herself. For some, it's really no more than this desire that drives them; they simply want security in a world that contains terrible powers, and they're willing to do whatever it takes, even brainwashing and murder, to remain safe and secure.
Some Seers come to the Iron Pyramid out of simple fear. The Exarchs are too powerful to be opposed, so much as they don't care for the order's methods, they feel they have no actual choice in the matter. Every unpleasant task, for some reason, appeases their mysterious gods and staves off whatever terrible Old Testament wrath might otherwise erupt.