Ideas and suggestions.

We just finished a game where churches had a decisive impact on the final result. There were two churches located right next to the opponent's two main cities.

Of course, you can argue that you need to capture them to prevent the opponent from doing so, and come up with some other strategies, but I have a different opinion.
I remember that at one point, I even had to agree to a draw because of the churches – it was impossible to defend the cities.

I think the right approach is to make them both costly and have a limited duration.
For example, the entrance fee to a church could be 1000 at the beginning, and increase by 1000 each time.
That is, yes, it's a strategic object, and it can sometimes play a very important role, but it shouldn't be infinitely free.