Not allowing discussion of something (including, if not especially, religion) should be the "bannable offense" by any intellectually-honest institution, especially given the significant impact that unsubstantiated religious belief has on the world.

The key to avoid flamewars (this from someone who has moderated many many discussions including those of a controversial nature) is to stick as close to facts and secular ethical reasoning as possible. Where there are no facts nor secular ethical reasoning to be found, one cannot impose one's view on others, and one cannot successfully argue any case, simple as that.