Perhaps there should be a chance that some of the militia side with the mob? Our perhaps some of the troops don't get there in time participate? Regions are big. No particular reason that *everyone* is just sitting there ready to help out.
I think it makes sense that the militia fights against the mob. The militia is on the side of the current region Lord; a mob is necessarily against. Also, it makes sense for a region Lords who is at risk of being targeted by priestly actions to raise militia as a defense.
The issue is more pressing for troops led by actual nobles. The problem is that a priest can be in the situation where he has friends with troops in the region, but would need to ask his friend to leave the region so he can act. This is counter-intuitive; it should never be damaging to have friends around.
I can compare this to the looting options. Defending troops will try to stop you from looting; however not all noble troop present will do so. If you go looting, it's helpful to have friends around.
Then again, I agree with other commenters: in a case where siding with your religions means going against your realm, it's not true that everyone will automatically choose the religion; however neither is it true that all would choose the realm. Since it's not possible to wait for each troop leaders to express an opinion (actions must be resolved at turn), I don't see any obvious solution.
