We live in a culture of values. Our culture has determined that physical abuse cannot be tolerated. Extortion cannot be tolerated. By making the choice to extort or cause physical abuse you are also choosing the consequences of that choice.
I suppose you are right, and unfortunately, emotional abuse is a lot harder identify and prove. Thus laws that prevent such abuse are not widely implemented.
Religious freedom does have some limits. You are correct, you cannot stone someone (physical abuse again) Someone choosing to shun you is not them encroaching on your liberty, they are execising their own liberty. The bottom line is they have the right to shun you. If I do not want to talk to you, for religious or other reasons, I can refuse to talk to you. I can even use our secular court system to enforce that you dont talk to me.
I would agree that an individual has the right to refuse contact with anyone they wish. (However, I also view doing so for the reason that you don't share the same religious view as being incredibly petulant.) It seems to me, though, that an organization had ought to be held accountable for its policies that cause emotional damage to people. Ah well, I don't expect they ever will be.