We have a live and let live policy about alcohol, pork, beef and other things that some religions regard as forbidden. Some countries don't, though. What's barred to them has to be barred to everyone else.
As things stand here and now, I'd expect Jehovah's Witnesses (a very small part of the population) would recognize that not everybody felt as they did about blood transfusions (apparently, not all Jehovah's Witnesses think alike on the matter, either).
Christian Scientists, for example, may not believe in many medical treatments, but Hobby Lobby doesn't mean that a company owned by Christian Scientists is exempt from the law. Most Christian Scientists (I think) recognize that the rules they apply to themselves aren't going to be accepted by the wider population as valid.
If I'm not mistaken I think what you're saying is basically the upshot of Hobby Lobby. The individual or government picks up the tab in the end, so it doesn't matter (though blood transfusions may be a lot more expensive than morning after pills, though). People who are intent on opposing the ruling will oppose and distort it whatever it actually says.
Trying to come up with ever more obscure religious groups and taboos, though, is a good way for them to attack the decision, so maybe it's not the right thing for us to do right now.
I had no intention from the start to attack the ruling, but rather my intent was to point out the law of unintended consequences.
And Fuzz was massively correct in post #16: SCOTUS made its ruling based upon the premise that the personal beliefs of the company were enough to deny insurance coverage.