the exemption is not carte blanch to discriminate any way that you want, which is how religious groups often want to interpret it.
"i have religious freedom! i can smite my enemies!"
nope. not at all. quite the opposite - these rules exist primarily to stop people from being oppressed by religion. that's really what a bill of rights is, a way to stop puritanical cromwellianism, and by extension any other kind of fundamentalism. but, we live in the time of orwell, so ideas are often mangled and manipulated into their contradictions, and the neo-liberal concept of "religious freedom" is a prime example of it. thankfully, our judicial branch is still operating, even if our legislative branch is slowly caving in on itself.
a religious exemption in the law has to be very narrowly defined as intended to protect the purpose of an organization. there has to be a deeply persuasive argument that the charter should be suspended. and, it is for that reason that the argument almost always fails....