What use are Great Prophet points if you already have a religion?
Great Prophet points are strictly for getting a great prophet (just like great scientist points are strictly for getting a great scientist). Being that you can only get one Great Prophet in a game, this means that great prophet points have no use once you've founded a religion or received a great prophet.
Holy site prayers do give faith so it's not entirely worthless. And it's pretty much the same logic for Exodus of the Evangelists dedication.