The churches have a reason for doing this. They are hoping to force the IRS to enforce the law so they can simultaneously cry persecution and seek to overturn the law in court.
So what can those of us concerned about separation of church and state do? Should we simply refuse to have the law enforced, or should be be preparing for a fight? As far as I'm concerned, this should be an occasion for activism.
I think this legal fight is going to happen sooner or later. By refusing to enforce the law, we are giving up without a fight. I don't think that is wise. Separation of church and state is too important.