It's not an easy issue, actually. This would affect religious orgs with government contracts. Accepting government money comes with it obligations that are avoided by not contracting with the Feds, in this case. Should a Catholic charity be allowed to accept government money and exempt themselves from rules that apply to all other employers who accept that money? And certainly if a Catholic charity can do so, so can any other employer who'd rather not hire the homos because of "religious convictions." And now you've got protections that mean little to nothing in practice.
I'm conflicted, but I don't think as a general rule non-discrimination in hiring over LGBT is a very high hurdle, outside official positions within a church. For example, I see no reason for an exemption for a Catholic hospital - if they want to accept Federal dollars, they shouldn't discriminate against LGBT in hiring.
"God is the name by which I designate all things which cross my path violently and recklessly, all things which alter my plans and intentions, and change the course of my life, for better or for worse."
-C G Jung
And if it's OK to not hire or fire a person for being gay, that is the kind of environment gays can expect. Keep their life hidden, because if the truth of their life is discovered, they risk job loss for no other reason.
Redneck, hillbilly, fundie, Bible thumper, cracker, split tails, geezer, loon, xenophobe, islamaphobe, and homophobe are not words of tolerance.
IIRC there are already about 21 states that include sexual orientation under employment non-discrimination laws. You might ask them.
In the other states you can flat out ask them. If they answer "yes" then you don't have to hire them. If they answer "no" and you find out later, you can terminate them for falsifying and application.
Another would be a company hires John, while completing John's hiring paperwork he applies for his spouse for inclusion in the company health insurance. The company let's him go.
the religious exemptions in the HL case was based on paying for products they believed were used for abortion ( don't argue the point, it doesn't matter if they factually are or not)
Obama would be in a good position to say " nope, no exemptions " and I believe SCOTUS would back him up on that.