This church is the only one in Paradise Arizona. You are tasked at one point in the game to go to the church and confess your (many, many) sins. Once there, after having spoken to the priest in the confessional booth, a group of Taliban decide to "take back their land" and attack the church armed with machine guns and rocket launchers. While you are not tasked to defend the church, you must escape from the church with the aggressive Taliban being in your way.
The next day if you return to the church you will find that the Taliban have taken over the church. This seems to happen regardless of what you do during the mission.