So, part of me is a bit squicked by the feds' attempts to force church-funded employers to offer counter-faith services as part of their employment benefits. I think it mostly comes from the standpoint of "keep da gummint outta things" feelings I generally hold to.
I think we've kind of moved (or at least those who have money to lose on the deal) from a country where you're "free to worship how you please" is being replaced with the supposition that "if I claim religion, I should feel free to act however I please, so long as I can site religious beliefs as my rationale."
When I look at the specific issues, it strikes me that the potential for conflict wouldn't exist if the potentially-effected organizations stuck to their operational cores. If they wanted to offer public services and chose to only people those service providers with people who were strictly volunteers rather than employees, there'd be no problems. In the capacity of a volunteer organization, indeed, the government would have no place to dictate acceptable compensation and benefits arrangements.
It's that these organizations have crossed from being volunteer-efforts to being employers that introduces the problems. Realistically speaking, as an _employer_, they should be subject to the same standards, expectations and legal obligations that any other employer is subject to. Even if the money for that employment comes from purely church-derived sources, it's still an employment construct rather than a volunteer construct. These organizations are already subject to other regulatory processes because of the industries they play in (just cuz it's "God's hospital" doesn't mean you get to ignore health regulations such as HIPAA) - so why should they be exempt from regulations surrounding terms of employment?
But, that's just my view on things. I don't really have any skin in the game, one way or the other (I'm not religious and I don't work for church-funded organizations - I'm just a tax-paying citizen).