I guess I have a pretty strong view on situations like these. People need to realize video games, movies, music etc... are not real life and should treat it as such. Even though the game takes place in real life towns and yes cathedrals that does not mean Sony or insomniac (the developer) has done anything wrong here. Fantasy is fantasy.
Anyone who is sick enough to actually hurt someone because of what they saw/did in a video game or some other form of entertainment was more likely than not unstable to begin with and would have found another source of "inspiration."
Freedom of speech is an extremely important thing, especially in a country who is supposedly based around it yet is having it quashed left and right by sources such as the government. Sony will probably pay the church off, which is more likely than not exactly what they wanted in the first place, just to make it look like they did the right thing but even that is more than should be done in my opinion.