Except that you refuse to allow the courts to strike down laws simply because it violates freedom of religion. That is your problem, not mine.
No, I actually want to see the law, or even just the contraception requirement, ruled unconstitutional and struck down. And if that was what Hobby Lobby is after, I'm in favor of it. But what I don't want to see, and what seems the most likely reversal (if any) to come from the Hobby Lobby case, is a special exception granted for designated religious institutions.
I don't believe the religious freedom guaranteed by the first amendment is intended to give religions special treatment. I believe it's intended to prevent it. It's there to prevent the federal government from making laws persecuting (or promoting) religion.
The stipulation that congress can't make laws 'prohibiting the free exercise' of a religion doesn't mean, in my view, that any law which conflicts with a religions practice can't be enforced if someone objects for religious reasons. I find that interpretation absurd. What it means, by way of example, is that we can't make a law banning Islam. But we
can make it illegal to marry underage girls or beat your wife, regardless of the recommendations of the Koran. And Muslims would have to follow those laws just like the rest of us.