I am certainly all for the idea of religious freedom, but I am also in favor of the separation of church and state. To me religious freedom means first- the right of individuals to make their own choices in regard to matters of faith and second- the protection of individuals from institutions gaining the power to enforce its dictates on anybody except those who freely choose to be a member, especially if that power is derived from public policy or state support.
While I am sympathetic in some ways to the perceived "war on religion" this particular issue seems quite out of the ordinary and is at best very cloudy thinking on the part of the church, or at worst a blatant political stunt or even (more frighteningly) a power play that involves the use of state power to enforce the Catholic Church's demands not only on its members, but upon many outside of its flock.
A few thoughts:
1) I would have more faith in the sincerity of the church's position if they had in fact already held similar positions or made similar demands on the one group it has a right to dictate to- its own members. Until the church announces a policy that requires its members to drop any health insurance they use that has contraception coverage or face ex-communication, I simply must question their motives for asking such a thing for people outside the flock. They will not do this because many of its members already disagree with this and freely choose not to comply, and would leave the church before complying. Since they are powerless to stop this, they are seeking public policies that enforce on people what people of their own free will refuse.
2) Furthermore, if the sin is no longer use of contraception, but any support of the general distribution of contraception even if to those outside the church, then it simply can not stop with health insurance. The church should require its members, (and latter everyone else) to not shop at stores that sell contraception, and stores that do not offer it, but use warehouses or distribution chains that support the sale of it, and stores that use banking and credit card institutions that are used by stores that distribute it, or travel on streets, roads, the internet or any other apparatus that supports the sale or distribution of contraception.
3) There needs to be a clear understanding of hybrid institutions. Catholic colleges and hospitals are not the same thing as Catholic Churches. They do not have the same rights to dictate to those who are a part of the those places as they do for their laity. They accept public dollars, federal and state aid, insurance (many of which offer contraception) and are built and function today because of the hard work and dedication of millions of non-Catholics- including Baptists, Methodists, Jews, Lutherans, Hindus, Sikhs, Eastern Orthodox, Bhuddists, Presbyterians, Atheists, Agnostics, Rationalists, Eupraxians,- just to name a few. All of them, and the employed Catholics themselves, would see their freedom on this issue seriously eroded. The church has a right to demand compliance from its flock, because they can choose to leave, but certainly they have no right to dictate to these other institutions and their employees, clients and patrons.
4) It seems to me that the religious freedom that the Church is arguing for is mostly about empowering itself to dictate to people it has little right to dictate to, and their asking to employ federal policy to do so. It is freedom of the church, not the people they are concerned about. The miniscule freedom from contributing in tiny ways to contraception for non-Catholics under health insurance in hybrid institutions seems ridiculous compared to the the use of state power to take it away from thousands that are not even members of the church, or against the appalling precedent of using public policy to back an institution's right to demand compliance from any group of individuals. No is being required to use contraception, you are being required to support everyone else's individual free choice in the matter.
It seems to me that this is not a case of a war on religion, but a war by religion. This is a war by Religious institutions against individual freedom and they are looking for the state to accomplish what they can not. If the state has one prime purpose, it is to protect the individual's rights to choose in matters of faith and their actual opportunity to make real choices.