Not that one should always have to compromise, but one model that may work OK-ish in South Africa comes to mind.
Constitutionally, clearly kids can't be forced to participate in religious studies, prayer meetings or the likes.
In practice I doubt that this is generally adhered to. My own child is lucky enough to attend a school that I think is really, really good at what it does, and there is very little I would want to change. But, he has confirmed that he didn't know that he is allowed to leave the class when Jesus is about to kick off. Would HE want to leave? Would Miss let him do so? Open questions, all, but I suspect things just work out this way due to practical considerations rather than a flagrant disregard for the law. Frankly, I too would rather have my child listen to Bible stories in the safety of a classroom than have him roam around in the yard for half an hour.
Still, I would be even happier if, for now, two things happen in traditionally religious schools:
1. They clearly define and set aside a period for worship applicable to the whole school.
2. Concurrently, a proper class offering alternative "entertainment" must be provided for. Such a class will be manned by either a teacher or a parent-volunteer (or a skeptic

), in which pupils can be told some interesting factual stuff, receive extra mathematics tuition, have discussions, or be entertained with science experiments.
I dare dream that such alternative studies could prove
so interesting that more and more kids will opt to attend them.
If a school wishes to continue practicing religion it will clearly be in it's own interest to set up such a classroom. That way the school can easily demonstrate that it is constitutionally compliant.
Rigil