You will be given the option to keep control over the city you have won or to give it to another faction (Emergent Kingdom of Jerusalem) if you keep it you will piss off the Pope, if you give it up you will gain lots of bonuses perhaps even start with KoJ as your vassal, but I think we can script lots of things like cashflow and even units. We are trying to create as many double-options or dilemmas for the player as possible so that the game feels more like a RPG or a simulation of rulership with all its problems and possibilities.
We are talking about about an option where you could instead choose to change your faction to the KoJ after a successful crusade.
Personally I prefer the first choice.