Yes, theocracies do have elections. Just onceevery other year or so, not every month. So yes you could get a bad ruler, but it will, on average, happen much, much less often. In fact, it has yet to happen for SA. Ever. I'd say that's a damn good set of examples to follow.
Also, I find that theocracy engenders a mindset in the players who have characters there. (This happens, more or less, in all government styles, too.) The people who play there go along with the idea of the realm dedicated to the church. It is, after all, a theocracy. So, no, there is nothing game-mechanics wise that forces the realms to fall in line with the church. It's the players who play in that realm that willingly go along with the whole concept that make it work.
So while technically just about everything you said is true, it's also all wrong. You are describing only the strict game mechanics. You have completely disregarded the player' willingness and desire to "play along" with the realm concept and idea. The whole SA phenomenon is based mostly on the players involved "playing along" with the theocracy and religion concept without needing any kind of game mechanics hammer to keep them in line.
