What are the limits of religious freedom?

What is your opinion of the recent Supreme Court decision, Burwell v. Hobby Lobby? A friend and I were discussing the case, and we disagree on whether or not the decision is good or bad. He views it as good because Hobby Lobby regained some of the freedom that they would have under an ideal free society. I view it as bad because while they did gain that freedom, it was granted to them for an incorrect reason -- exemption from the law due to religious beliefs. Does this distinction really matter? Also, should individuals or corporations be allowed exemptions from laws that interfere with their religious beliefs? Should religious beliefs be treated any differently than non-religious beliefs under the law?