About theocracy and non-state religion missionaries.
In the present rule set, theocracy stops the natural spread of non-state religions and stops the foreign missionaries from spreading a non-state religion, but it doesn't stop the state itself from actively (through missionaries) spreading a non-state religion.
The description of theocracy in the civilopedia is extremely short. It just says 'no Non-state religion spread'. It seems people are saying this means that missionaries from other religions should be unable to spread the religion but it doesn't explicitly say that.
Or to put it differently, how would you describe the present rules in one short sentence? The effects of the various civics are all described in very short sentences and these sentences often don't exactly describe what the civic does. Only through experience with the game have we learned what the exact meaning of the civics is.
Another example of a vague description: The holy shrines of the various religions say 'spreads religion'. This doesn't mean that the shrine builds missionaries which go to the various cities. It means that the existence of the shrine building increases the likelihood that the religion spreads naturally to cities that don't already have this religion. But this meaning is not very clear from these 2 words.
Since the description of the theocracy civic isn't very elaborate and detailed, I don't have problems that the state itself can actively spread a non-state religion.
By the way, if you take this ability away from the theocracy civic, then you'll weaken it a little. I don't see the need for that as in my opinion, organized religion is the strongest religious civic. Opinions may vary on this, but it's at least not clear that theocracy deserves a nerf.
On the other hand, I do think that the AI behaviour of automatically using the missionary that they very gifted is a bit buggy. They should consider whether that is a wise decision.