As with all laws and governance, granting religious freedoms as opposed to freedoms of every ideology strikes a balance. Religion presents a widespread, structured set of beliefs. The structured part makes it easy to enforce a law of religious freedom, because there is a vast body of source and interpretative work to use. The widespread part means that you are making a concession to a significant part of the population.
There's nothing arbitrary about the choice - it is precisely because religion is both structured and widespread that makes it a good candidate for such a law. Another example of a widespread belief that tends to get exemptions from many laws is freedom of speech(e.g. exemptions from defamation, copyright).
Religion presents a widespread, structured set of beliefs.
I'd rather say that religion presents a social identity, and prescribes a set of beliefs. The identity is what matters more to most people than the beliefs.
However structured it may be, you still end up with a set of arbitrary limitations based on majority rule. I agree with the GP that if some religious conventions are innocuous enough that they can be allowed for a part of the population, then they should be allowed for all, regardless of social identity. And if certain conventions are deemed dangerous, they should be disallowed regardless of religious sanctity.
There's nothing arbitrary about the choice - it is precisely because religion is both structured and widespread that makes it a good candidate for such a law. Another example of a widespread belief that tends to get exemptions from many laws is freedom of speech(e.g. exemptions from defamation, copyright).