The thing that I see missing is all this is what about the RIGHTS OF ALL EMPLOYERS (not merely religious institutions).
Why should a Roman Catholic hospital be exempt from going against conscience, and individual employers are not?
Why should an evangelical, or Roman Catholic, or heck, and atheist, business owner be forced to pay for services of any kind—especially if he (alone...as he is paying the bill...) considers them unethical?
So now religious GROUPS are more free in their conscience than individuals? What kind of 1st Amendment protection is that—which leaves individuals out?
Exactly. This is what the Progessive/Liberal/Democrats want to do. They wish to eliminate individual rights and replace them with a socialism that expresses Progressive/Liberal/Democratic beliefs only.
The biggest trouble I have with that socialism is that it is strongly atheistic and strongly anti-Christian in it's current form. Christians are singled out as 'Extreme' and 'out of touch' right wingers who need more liberalism. It's gotten to the point where this administration is trying to label them as terrorists to be put in the jails at the very least.
So you are exactly right, it is an attempt at wiping out individual liberties and rights.