If I was in your situation, I would explain to the entire class that when we are all born, we do not pick the family, and the respective religion of that family that we are born into, so even if one religion might be viewed as "better" than another religion, it is not a person's fault for being born into any particular religion.
And, since making negative comments about any religion can offend a person that might either be that religion, or perhaps have family or friends in that religion, all comments should not be shared in class.
The problem, in my opinion, is not one specific person, as you seem to believe, but a lack of regimented control over the class, where one person finds it acceptable to offer his gratuitous comments, or confer with "buddies" to do his bidding.
I obviously do not know the level of discipline that your school subscribes to; however, there has been more than one movie, I believe, that highlighted how a Parochial School, in days gone by, was known for the level of classroom discipline that was maintained, and parents sent their children to such a school for the benefit of having their little darlings learn how to control themselves, so one day they could become contributing members of society by knowing how to act in a superior/subordinate situation.
So, I am not offering advice. I am just saying what I think the problem is, and perhaps in today's society, in your school, my thinking is not acceptable? But, as I was told years ago, there were not many problem children in a class of Jesuit priests six foot or taller.