I've now read the Hobby Lobby decision. I was prepared to hate it. I now merely find it unpersuasive. Alito did a much better job of defending his position than I expected him to (and I actually expected Scalia to be the one writing the opinion). At the end of the day, though, there's a major policy problem that the Court did not address, that needs to be addressed.
The First Amendment contains two religion clauses: Congress shall make no law respecting an establishment of religion (the Establishment Clause), nor prohibit the free exercise thereof (the Free Exercise Clause). Neither exists in a vacuum; they have to be read side by side. Simply put, the first clause means the government can't give religion special favors and the second clause means the government can't give it special burdens. It may neither treat religion favorably nor unfavorably. Religion is a private matter, and religious belief should not result in either good treatment or bad treatment from the state. The state is supposed to stay neutral on the subject.
I have enough libertarian instincts that I'm not entirely opposed, depending on the circumstances, to allowing people to have conscience exemptions from some laws at least some of the time. But if the government is going to give conscience exemptions, it has to do so in an even-handed manner. It shouldn't be giving them to religion but not to the non-religious.
Suppose an atheist starts a business. Neither he nor his business will be entitled to any conscience exemption to any law that he finds morally objectionable. It does not matter how deeply offensive and repulsive he may find a law to be, or how good a moral argument he can muster against it. His conscience doesn't get him any favorable treatment. He has to obey the law or face the consequences.
But let him come along and say that he has an objection based on a conversation he had with a ghost, and suddenly his objection becomes religious and gets all kinds of special treatment.
Now, I hasten to add that there are perfectly sound policy reasons not to give anyone a conscience exemption, because once that starts, anyone who doesn't want to pay taxes, or hire blacks, or refrain from sexually abusing children discovers some religious hook or other on which to hang his objections. If I can ignore the speed limit just because my religion tells me to, then it won't take much for me to find a religious argument that I'm supposed to drive 90 miles an hour down I-90.
But if the government is going to start giving conscience exemptions, then it needs to play fair. Secular consciences are entitled to as much respect as religious ones.