The argument behind the question is “Shouldn’t we just all ignore religion based morality and set our government policies on what the majority wants?” Right? No? ARE there basic moral principles that must guide governmental policies or is everything up for grabs on majority vote?
I would assert that we had BETTER keep in mind the presence of objective right and wrong or we will soon be in the hands of totalitarian leaders who will manipulate their way to a majority power and then use that to dominate the weak.
So the question is NOT one of whether we can make exceptions for any and all religious ideas, but one of identifying the public good intended by the government policy and then evaluating objections to it individually based on the merits of their arguments. Where an objection is solidly and clearly based on basic human rights, the policy may need to be overturned entirely (i.e. Roe v Wade is an example). Where an objection is reasonably disputed and there are reasonable alternatives, exemptions should be granted (buy your own damm contraception, freeloader!). Where an objection is based on an arbitrary religious teaching and the consequences of exemption would likely be severe, it may be warranted to deny the exemption (Hey, smokin’ peyote is part of our religion, dude!).
In answer to your question, the JW blood transfusion issue would fall in the third category. They should be allowed an exemption for their own institutions (church employees, schools, etc), but individual employers should be required to provide the coverage. A reasonable accomodation would be for that employer NOT to cover it in the basic coverage, but offer it as an extra cost rider to individual insurance policies.
So what about a catholic employer? IMO, this falls in the second category. Reasonable people can reasonably dispute the way in which contraception defies the basic moral order of society. Since it’s disputed, there must be a compelling public health interest to in order for government policy to override the religious conscience of an employer. In this case, there is a clear and simple alternative to contraceptive coverage: go buy your own you freaking freeloader. Condoms are what, $5 for a 3 pack at every drug store and gas station in America? You can seriously keep a straight face and tell me it is a compelling public health need to make hormonal contraception “free” for all? Give me a break.