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.
It's interesting that these colleges are investigating these groups so carefully. They want to know exactly what you believe, and if you don't believe what they believe, then you get bounced.
Somewhat Orwellian, but maybe it's because they are bound to give funding to these groups if they give them a charter.