The whole argument under the Free Exercise Clause doesn't make sense because the directive not to discriminate against gays is not specifically aimed at a specific religion, its generally applicable.
In practice the Free Exercise clause makes it illegal to pass a law restricting a specific religion. What really pisses me off is how these people don't even understand one of the most easy to understand clauses in the Constitution. It is well settled that Courts and lawmakers can prohibit religious practices, e.g. ritual sacrifice.
Granted, that doesn't mean they can't pass the law invalidating the protections, but the underlying premise is faulty.