The notion that religious institutions must cover birth control is false. Employers cover nothing. Insurance companies do. Employers sometimes subsidize the cost of insurance for employees. If Catholic and other religious institutions object to subsidizing birth control, then it should still be available as an add-on at the employees cost or as covered by the government's new Affordable Healthcare Act.
I believe it is absurd to think that an religious institution should have to cover birth control. Religious institutions are there for people to grow spiritually and take part in a community, they should not be intertwined with your health concerns. This question oozes with entitlement problems. Birth control is a personal matter and a health matter, it should not be directly tired to religion.