While the court said that to use religion as an excuse to not cover some contraception was fine, they also said that religion couldn’t be used for any other decision making process, only contraception. I’m sorry, but that seems odd, and I’m not sure if future courts will see the difference. How can you limit freedom of religion so minutely? Plus once you hint at a right, no matter how narrowly worded, it will be used as precedent, and will probably cause problems in the future.
Of course it may never come up, but the history of Supreme Court decisions, and what is used later on, is quite surprising. It could bite us in the future.