merubhanot, if you keep an inquisitor in a city then you can't be religion bombed. It can still spread naturally, but its not that hard. to keep on top of that. The only downside to that is you have to take them out if you want to purchase a worker/settler, but I haven't seen the AI keep a missionary / great prophet in my borders for longer than a turn once they notice they can't do anything- they always seem to go bomb something easier.
In regards to the OP, I spend my faith on getting Great Prophets / Great Artists and littering useless tiles (such as Snow or middle of the desert) with Holy Sites / Cultural Doohickeys. Coupled with the Freedom Policy Finisher, you get a ridiculous amount of faith / Culture, and you just spend the faith on getting more Great Prophets/Artists, and topping off friendly city state culture when you want it.
Admittedly, I don't tend to go higher than Prince unless I'm OCCing, but it works for me.
- Micael