Sort of. Religious organizations can still discriminate. You can't sue the Catholic Church, for instance, for not hiring female priests. The question becomes does religious freedom only apply to organized bodies and their pursuits or does it apply to the individual and the individual's pursuits.
Yeah but that is technically a leadership position in a private organization. This is specifically with regards to discrimination of patrons of a business. You are conflating religious freedom with utilizing that religious freedom to selectively discriminate. I would argue that religious freedom was not intended to allow you to affect others with your religious beliefs, only protect your ability to worship and follow a specific flavor of religion. However, it becomes a chicken and egg issue then. If my religious beliefs prohibit me from doing some certain thing, and I have a business that caters to the public, how is it fair that I be forced to perform that certain thing in a way that goes against my religious beliefs which indirectly affects other peoples ability to get services.
I think that the reason that people have such a hard time with issues like this is that as America becomes increasingly non-secular, people are having a harder and harder time reconciling peoples religious beliefs as something that isn't malleable. I would argue that religion has brought some of this upon itself, due to its shifting away from the rigidity and dogmatism. Once you have shown that you are willing to move the goalposts of what God supposedly wants, what is one more shift on something that to many seems relatively benign? Now mind you, I don't think that this is solely religion's fault, as much of society has changed, but I do believe that the perception factor by a growing non-secular society is increasingly putting anyone who steadfastly holds to religious beliefs as bigots, and everyone else is apathetic. This is likely due to the language that comes out of the two camps who really have a dog in the fight being on such polar opposites of the messaging spectrum.