One thing that we have to keep in mind is that Hobby Lobby is a retail establishment and NOT a religious organization. It is subject to the laws and regulations of the government, religious organizations have exemptions from some of those laws. Hobby Lobby wants to deny benefits to its employees based on the founder's religious beliefs. But, it employs thousands of individuals making it subject to federal discrimination laws and it likely receives tax and other incentives from the government. Because of this, by allowing them to opt out of a federal program based on the religious beliefs of its founder, you are opening a huge can of worms for other large companies who will have an argument that because something goes against the religious beliefs of its CEO or President, including those who choose to discriminate on the basis of age, sex, national origin, disability, etc. Should a company be allowed to pick and choose the laws to which it should be subjected?
Again, regardless whether I agree with the founder's beliefs, this could open up a pandora's box on lawsuits against employers and the government.