Is it just as wrong to make policies that discriminate against the majority as it is to make policies that discriminate against the minority? Should the government deny the majority health care services on the premise that it might go against a minorities’ beliefs?
As for religion and state, the government is charged with due diligence to protect the life, liberty and pursuit of happiness of The People. It has not been charged with protecting the liberty of religious organizations. While religious organizations are made up of people, they are not The People. The First Amendment protects the free exercise of religion, and mandating health coverage does not impinge on the exercise of faith. It does not require any one to use the coverage, only for organizations to provide it for those who choose to use the coverage.
In the end, it comes down to money, or in other words taxes. Whether the tax is levied in the standard sense or through mandating organizations to cover heath care equally, it is still a tax. So rather than arguing about contraception, maybe the argument should be on whether religious organization should lose their tax exemptions? This change has been called for, but I think that our churches would prefer simply offering health care, it would probably be much less costly.