I know this will be unpopular, BUT, if Hobby Lobby is a registered corporation then it is a creature of government. You can't have 2 masters(God and the Government), once they incorporated the business, it(Hobby Lobby) became a servant to what government wants it to be. You can't keep expecting to receive the benefits of incorporating and not expect government to enforce what it wants in return.
They contracted, now they should obey the contract or find a different way of doing business.