Protestant players weren't affected by those reqs, except maybe for Sistine Chapel and Escorial. All the other wonders are already built when Protestantism arrives.
The problem is that it was not occasional. Even with higher cost for wonders, Byzantium and Arabs have a huge scientific advantage. They will always end up building some of those wonders. I think that will happen even if you make it less likely for them to build.
They have far too many turns.
And it required the religion in the city, not as state religion. It wasn't so restrictive.
I put it not as a question of religion involved historically, but of cultural groups.
Anyways, I can always keep the old file and play my games with it.