I am a pretty militant atheist myself, but even so, I know how to conduct myself around other people. Philosophy or degree of philosophy doesn't really matter when interacting with a group of people. What matters is behaving oneself in the group. Calling people names or being generally disruptive is offensive in any setting.
I think this person needs to be told they're acting inappropriately soon, or your little group is going to disappear. If you're uncomfortable confronting or speaking to him (that's okay, most of us will go pretty far to avoid confrontations), how about at the next meeting handing out a general list of rules for the group? This can include how to pass out information, how to engage politely in debate, and all sorts of things. Then if s/he still doesn't get it, you can do the confrontation thing. Then maybe you can get those who left to come back and give it a second chance.