I feel like the title of this was a bit misleading. Your not really arguing that Christians shouldn't play video games, what your arguing is that Christians (or any religious person for that matter) should get upset with subversive (in their view) forms of media because they could actually learn something from it (which I would agree with btw).
Personally, I'm a atheist but I don't find this discussion very fun or enlightening. Religion just seems like a very personal thing and I wouldn't presume to tell others how to feel about their religion unless they get preachy and righteous about it then I have no problem telling them what I think about their god or gods. When you don't respect my ideas or beliefs then I don't have to respect yours (but honestly this only happens to Christians with me when they find out I don't believe in any gods. Most other religious people seem ok with it in my experience).
I think its actually kind of commendable that the guy left the project. Better that then to force a creative change or make the work environment really hostile or uncomfortable because of your beliefs. Too bad more people aren't like him.