I've always wondered why Autodafe requires a temple of a certain level, yet there is not requirement to have a temple in the region for declaring a religious state. Troops of any kind make RTO's rather difficult, and there is the loyalty restriction, but I think requiring a temple of the religion might be a good thing as well.
May as well scrap the option altogether, while you are at it.
It can only be declared by an elder in a region with 80% following. It's pretty darn difficult to have 80% following in your own regions, never mind enemy regions.
Religion spread is easy to fend off. Maybe not the first 40%, but it's rather easy to keep no higher than that. If you let foreigners control your peasants like this, you deserve to be at their mercy.
Then there's other cases like Hvrek, where the other old faith died and he got a lot of lingering power over Riombaran regions. Suck it up. This is the result of Riombara giving great freedoms to the Order of Alluran for quite a while now, it wasn't done overnight. Be careful who you give such powers to.
This is, imo, the only way for religions to have any sort of tool to defend themselves. They deserve it. Without it, religions are defenseless. Because really, except for small depopulated regions, the only real targets for RTOs are long-time assets of the faith. It's not really a tool of aggression, but rather a tool to protect one's assets against realms and lords who can otherwise crush years of efforts with impunity by just clicking a few buttons.