Religious Exemptions Are Inherently Flawed

Ed at Dispatches has a post speculating on the limits of religious exemptions to various and sundry laws. He asks whether there's a coherent legal standard that can be applied in such situations. I'm surprised he's even entertaining the question; it seems pretty clear-cut to me that no such standard exists for the following reasons:

1. Such regulations require the government to make judgements about the validity of religious beliefs.
2. Such regulations show preference to religious over secular beliefs.

Isn't this exactly the kind of religious vs. secular entanglement in which the government is supposed to avoid getting involved? Consider item 1: Let's say I'm a Discordian, and I want my employer to give me Fridays off because that's my holy day. If government intervention is required then this situation puts the government in the position of judging whether

1. Discordianism is a legitimate religion.
2. Discordian scripture really requires me to take Fridays off.

The above example is certainly contrived, but is none-the-less valid. Determining which religions are worthy of recognition is not an appropriate function of government. Incidentally this is also why I think tax-exempt status for religious organizations is a non-starter. Regarding item 2: Suppose I'm a pharmacist with an ethical (but secular) commitment to zero population growth. Can I refuse to dispense fertility drugs? Suppose that I have a deep and abiding commitment to the elimination of ignorance. Can I deny medicine to the willfully ignorant? Why are my personal concerns any less valid for having secular roots? If the government is going to allow exemptions at all it needs to frame them as a matter of personal conscience rather than as exemptions specifically for the religiously-minded.