They aren't a theocracy. That pissed off a lot of people. They were stubborn, bull-headed, and self-righteous about ut. Now they are paying for it. Case closed.
Not quite, imo.
Seems like it comes down to FR's self-determination versus Church-determination. I can't blame FR for wanting some self-determination after all Allison's shenanigans. The more bull-headed party here seems to be the theocrats. The shield-banging didn't really squash FR's independence-streak, it just inflamed it.
In summary, there's no guilty party and no innocent party, just a bunch of people butting heads over power. Good ol' SA doing its job as our Dwili Catholic Church.