Why should free exercise of religion be defended? Not because people can make wrongs right just by thinking that they are right, or because religious folk would like indulgence for private eccentricities, or because they would like exemptions from reasonable demands grounded in the common good.
No, free exercise is an element of the common good, grounded in our shared human nature. As a rational being, man is ordained to know the truth, especially the truth about God; knowing the truth requires seeking it; and a certain liberty is necessary even for the search.
The common good has other elements too; religious liberty does not justify violating the natural law. Even so, the burden of proof for regulations on religious liberty should be on the state. Why? Because governments make people do all sorts of things that are objectively wrong, and because even an erroneous conscience deserves some consideration -- not because it is erroneous, but because it is a conscience.
So on one hand, the claims of conscience must be exercised within the bounds of public order, but on the other hand, "public order" must be understood as the common good as viewed in the light of the natural law -- not as a synonym for whatever the government wants to do.
Any lawyers out there? The real challenge is to figure out how to make coherent arguments along these lines within the incoherent framework of First Amendment religion clause jurisprudence.