[@shylarah] I don't think I ever discussed this but, inquisitors do answer to a higher authority within the Church and thus they can't just do whatever they want.

 I think there are different branches of the Church, one being the clerical branch and the other being the military branch. I did use the term "lesser branches" when referring to students who were transferred because they couldn't cut it in the Red Seminary, but that's only in the eyes of inquisitors who are trained to fight. The clerical branch is actually the ruling hand of Varya, so they possess a lot of power over governance and scripture and all that-- i.e Magnus being a vicar of the clerical branch would have the role of a governor or something similar within El (once it is conquered and the first colonies are established).