They're acting like a religious organization.
If you think they should be punished financially for requiring students to keep to the tenets of their religion in and out of school, I wonder about your real motives.
But fine, tax their asses off. Maybe the government would like to then cough up the money that won't be available for the hospitals and charities that the Catholic church won't be able to afford to run anymore.
As far as I see it, if they're getting special financial consideration from the government, it's as good as getting government funding. Government-funded institutions have to respect the Constitution, and so should they.
Frankly, I would question the priorities of any institution that would rather shut down hospitals than respect its members' rights and privacy.