Hobby Lobby really has no leg to stand on here. Yes, they are entitled to their religious views but they are not or at the very least should not be allowed to have them dodge their legal responsibilities.
If they fuck up and actually let them get away with this, I have a feeling in the not too distant future we will have businesses owners claim their religion shuns modern medicine in favor of pray healing as an excuse to avoid paying for health insurance entirely or to pay a smaller faction to a church in return for prayers for their injured workers.
Church should remain separate from State and Business for such decisions for a very good reason.