There are two problems here. First, the religious fundamentalists aversion to science. And second, the implications of business claiming to have religion and then being able to claim that said religion exempts them from the law. I'll tackle each separately.
First the morning after pill, is not an abortifacient.
Doctors consider that a pregnancy starts at implantation. Some religious folks believe that life (not a pregnancy, but life) starts at fertilization. Which means that God is killing babies (tiny, helpless, single-celled babies) at a startling rate (50-60%!), as a ton of these new lives end before people even miss their period. (WHY, God, WHY?! Why do you kill these babies so much?! And yet your followers demand that women protect these single cells way more than you do? And with hardly any evidence to back up their methods?) For example, these religious folks say that if Plan B prevents implantation, then Plan B kills a "baby." Luckily, there is science for that. And it says, that, no, Plan B doesn't prevent implantation. It prevents ovulation. And that is precisely why Plan B isn't effective at preventing a pregnancy if you've already ovulated. And also why Plan B doesn't kill "a baby!" But it is hard for some people to unclutch their pearls. And besides. Science is hard. Screaming at the ladies about how to control their bodies is easy!
Yes, what happens? What if Hobby Lobby opens that door. Then we can all be discriminated against by any old (or new) religion. Not cool. Sorry, Hobby Lobby and Focus on the Family, you're not a person. Jesus doesn't love you. And Plan B doesn't kill babies. Get over it.