Last weekend, I actually did finalise and send off my submission to the current project on freedom of religion and belief (being conducted under the auspices of the Australian Human Rights Commission). I can't think of many more important issues for our Western societies than what kind of freedom is granted to belief of various kinds. The more I've been looking at this issue, the more I conclude that there have been tendencies to make it include both too much and not enough. The tendency to make it include not enough comes from the pressure for only "nice" beliefs to be given freedom. I say that, absent some compelling justification, we should be free to believe whatever we want, not just whatever nice ideas we want. This dovetails with freedom of expression - we should be free to express our beliefs, not just nice beliefs. For example, it used to be popular in fundamentalist Protestant circles to believe that the Roman Catholic Church is the "Whore of Babylon", described in the Book of Revelation. I'm willing to bet that there are still plenty of fundies who believe that. It's a particularly stupid doctrine, and certainly not a nice touchy-feely one. But they are free to believe it, and should also be free to express it.
At the same time, there's a tendency to make the doctrine include too much. You can believe whatever you want, express it, conduct your rituals, and so on, and there should be no limit to what beliefs, doctrines, organisations, rituals and so on are protected. Except it's not a get-out-of-jail free card if you break secular laws that have general application. If the objects used in your rituals attract sales tax or the GST, you must pay it when you purchase your paraphernalia - just like everyone else. If your rituals involve human sacrifice, you'd better modify them, because religion doesn't exempt you from the ordinary law applying to murder. If you practice as a medical doctor, then you are in a position of power vis-a-vis your patients, which requires that codes of medical ethics be put in place to protect patients from doctors who, for example, want to impose their own morality on their patients' lives. You must follow the code of ethics, even if some aspect of it conflicts with your religion.
I'm not against some reasonable flexibility in the laws to accommodate people who might be seriously disadvantaged for any reason, religious or otherwise. Moreover, part of the problem is that there are so many laws around that cannot be justified at all - they look particularly harsh when they cause problems for people with religious beliefs. But the solution isn't to extend the political principle of freedom of religion; it's that the state should stop enacting and enforcing laws that don't have a clear, legitimate, secular justification in the first place. In the criminal sphere, legislatures should stop enacting prohibitions that can't be justified against the harm principle (and some cautious, principled extensions of it). All of these principles - freedom of religion, freedom of speech, and the harm principle - are consistent with each other, and indeed they dovetail nicely. But that's on the assumption that we give them all full effect while not making any of them do work outside what they actually cover.