My point of things not making sense has nothing to do with SMA. I get the whole "if she burns, she's not a witch" thing. Rather, what will happen is that your religion will turn off players. You will be accused of being corrupt, power-hungry, tyrannical, etc., and you will alienate those who are the most powerful people in the realm. The realm government won't like you, because cities are so important for the realm. Destabilizing and/or destroying a city will piss off too many powerful people, especially if they are in a foreign realm from the church's power base.