I mean, I honestly feel that a full range of family planning services is an essential part of women's healthcare. So... shouldn't the government direct insurance companies to cover family planning? But in that case, why have any exemption at all for churches?
I mean, if the Church of Red Asphalt has a philosophical objection to seatbelts, that doesn't stop the government from making laws that automakers have to follow. Those laws don't affect individual consciences or the tenets of the church.
If some nun wants to go on the Pill, it's no business of mine to help enforce the Church's will on her, that she not use BC, or if she does, she's damn well going to pay full price for it. She has her own conscience, and presumably knows what she wants. And if the Church finds out, they can always fire her or defrock her or whatever, like the Catholic school that fired the teacher for getting pregnant through artificial insemination. (Yay, religious liberties!)
I guess the problem is if the Red Asphaltists take their convictions so strongly that they forswear cars. Analogously, if churches or religious organizations stood on principle and dropped medical insurance for their employees, that would not appear to be a good thing, either. And this would conceivably apply not only to churches, but also the other religiously branded organizations currently under discussion.
(However, since many states already require this sort of coverage, presumably this is not what would happen.)
As a more realistic analogy, the Jehovah's Witnesses do not accept blood transfusions, even in life or death cases. This is a "non-negotiable religious stand", and JW's generally ostracize (former) members who undergo such procedures. Although their religious stand is quite clear, I don't think they are exempt from offering insurance that covers transfusions. Should they be? I don't see any difference, except that people get a lot more excitable when we start talking about lady parts, and what ought and oughtn't to be done with them.
Can I start my church that has as its central dogma that medical treatments that cost more than $100 are anathema? Can I then get really cheap 'medical' insurance to offer my employees?
Do we want the free market to decide what procedures insurance companies offer coverage for?
If not, and there is some sort of established nucleus of medical procedures that must legally be covered, why shouldn't birth control be part of that?