I think the problem
here is that unless
there is religious framework
in place you are always going to get people in the assembly
who would rather not be there and praying
. I must say that I attended a school where Prayer was compulsory
at least twice a day, once in morning assembly, and once at grace
at lunch. I didn't mind either, even though I was (heck, still am) Muslim
I was lucky, in our school the emphasis was on genuine thanks and respect for what we had received (it was quite a posh school, but full of nice people) , and there was nothing at all sectarian, or holier than thou about it. I usually participated in the prayer, modifying the solely Christian bits cos they aren't particularly Islamic, and prayed to God anyway. I didn't mind. I was the only Muslim there. Still, that being said I would have liked the option of praying privately when my prayer times came around, which wasn't available then.
I think schools should make provision for people to pray if they so wish, and they should be given the privacy and respect to do so. I also think that religious practices should be protected, no one should ridicule another's way of practicing faith. I also believe that schools themselves should be free from the sort of religious fundamentalism that eats the hearts out of many teenagers and disillusions them to their society.
Religion is a very positive thing, especially when given room to grow peacefully. It is only when they feel under attack do religious people become belligerent. Lets make sure that doesn't happen.