I agree with most of what you say. But you can't make an exception for one group, no matter who they happen to be. Other groups will want to meet in the Commons area too. Even if it isn't disruptive now, the end result of letting one group meet there will be.
Possibly, and it would make sense to issue a blanket policy if and when that happens. Frankly I doubt it would, because the more groups meeting there at the same time, the fewer would find it a suitable place. It seems to be working for the prayer group now, but I imagine if a couple dozen other groups were all meeting there at the same time, including some loudly debating groups, they'd choose another spot. I have to think, though, that the cafeteria in a school this large, could accommodate quite a lot of students without any interference in "traffic" or other school operations. I mean how on earth do they manage the "traffic" problem at lunchtime??