A ping for your well-considered thoughts on this topic.
On the one hand the danger of people concocting a religion to avoid the application of law is obvious. On the other hand if we permit people to opt out of a constitutional law by permitting a religious group to scruple over a law, we have then to permit the courts to decide as a matter of law what a religion is or is not and what observance a religion is or is not entitled to have protected. This is a very dangerous path.
However, it is a path we go down when we decide whether someone is a legitimate conscientious objector in time of war, for example, so it is not something entirely beyond the canon of our justice system.
My bias in this case, of course, is to favor the religious liberty of the company involved but we have to be careful not to let hard cases make bad law. Certainly we have bad law, Obamacare, making more and more bad law as the court twists and perverts the Constitution to declare it a tax or, for some Justices, perfectly acceptable exercise of regulation under the commerce clause. In other words, when you start to go down a road created by a bad law it just gets worse and worse. There is no reason why we should be confronted with this dilemma. The real constitutional crime here is Obamacare itself.