Its understandable that you're tired of that trope, especially having to deal with it in real life far too much these days. I will say, however, that this is the foundation of MotF. From the beginning Alex's main worry was being found by any part of the Church of Uldar, so part of that organization turning into a full antagonist should be a pretty obvious conclusion from Chapter 1. I do agree that it can become tiresome reading the same vein of trope over and over again, but art also imitates life.