Its functionally very similar to losing all faith.Is "losing the cost of a great prophet (or all faith if you don't have enough)" a possible solution?
I'd suggest
A) Controlling a holy city increases the cost of future great prophets. So if I conquer a religion, I still have to pay the normal price of 1,100 faith to enhance.
B) When you conquer a holy city and you don't already control one, you lose half of your faith, instead of all of it.