It should be undisputed that the government ought to prohibit certain practices on the grounds that they're inhumane. NFL star Michael Vick spent 21 months in prison for his involvement in a dog-fighting ring. People apparently disagree about the particular practice of kosher slaughtering.
If the government decides to prohibit it, then it makes sense to try to accommodate the people whose free exercise of their religion depends on it, and to make an exception for them. But that necessarily requires that the people entitled to the exception be identified.
We have something similar in the U.S. The Amish have a religious objection to Social Security. When Social Security was extended to agricultural workers, at least one Amish farmer went to jail rather than pay FICA taxes. As a result, the law was amended to provide an exemption for the Amish, but it had to be narrowly tailored. If a bunch of libertarians were to start a "church" that hails Ayn Rand as a prophet, they wouldn't qualify.
Accommodating minority religious views leads to difficult problems sometimes. Governments could just say "the hell with it" and imprison Amish farmers while making it impossible for some Jews to get meat. Or they could go to the other extreme and say that anyone can get an exemption just by asking, meaning that the laws mandating FICA taxes and prohibiting kosher slaughtering are, in effect, dead letters. The only way to avoid those unreasonable extremes is to give some people a preferred status, based on their religious views, and to couple that discrimination with a mechanism for identifying the ones who are chose (pun intended). Of these three bad solutions, the last one is the least bad.