If I understand this right, the owner of Hobby Lobby claims the right to dictate the "morality" of the company. The way I see it, the owner abdicated that right when the company was incorporated. By removing himself from liability for the company while still controlling how it "thinks," he is trying to have it both ways.
That's just the way I see it. The real world may see it differently, and the American legal system, which lives in yet another world only tenuously attached to reality, will have its own point of view.