Do they also deny charters to Jewish and Muslim groups? If not, then I think it's clearly discriminatory.
That would only be the clear cut case if that groups rules, as the Christian groups do, requires that members be of that religious background. The story stated that the groups charter required that members be Christian. If the Muslim group's charter has a similar requirement, then we have a definite contradiction. Same would be true if the gay group's charter stated that all members have to be gay.