Doesn't this argument sound a lot like the "Well I have no problem if the fag stays in the closet, but they shouldn't go around parading or being gay in public or together or anything" that a lot of bigots say?
Then what should they be praying for?
So you don't believe that any club or group should meet anywhere on school property? Or does this bigotry only apply to Christians?
As long as you aren't praying for your friends, school, or nation - of course.
Comandeering? Are they coming with rifles and bayonets and raising the protestant flag?
If your friend was specifically denied the ability to have a group just because it was Buddhist, then that is clearly discrimination and you should file a law suit. Though I would probably deny the request for such a group with that name as the name either A) mocks the name of the Christian group or B) mocks a central belief of the Buddhist faith.