That is a fascinating article. I have seen some of those arguments debated on this forum, but it was great to see a thorough and scholarly discussion of these issues.
I think that part of the problem is that it is much easier for a court to dismiss a case based on the idea of preserving the rights of a religious organization than to interfere in the interest of preserving the legal rights of the individual.
It would take a clever lawyer to overcome that hurdle, but I could see it happen in certain shunning cases if the lawyer puts the proper emphasis on individual rights.
I'm not religious, but I believe in the value of personal religious liberties. I resent that the courts have so consistently favored the rights of organizations over the rights of individuals. The result is that if a person tries to exercise his freedom of religion by joining a religion, then he must surrender some his rights to the religion itself, according to the way the courts have been deciding these kinds of cases.
It makes little difference if the religion is moderate and tolerant. The religion can arbitrarily change its policies and the courts will be unlikely to intervene if this harms the members or interferes with their right to leave freely.
I also think it's necessary to distinguish between a person's right to shun and the enforcement of shunning policies by church leaders. I don't think the courts should interfere with personal shunning, but there should be a legal remedy if someone uses his influence to compel others to shun. So an elder, for example, should be free to shun a former member, but if he sits on a judicial committee and punishes a current member for associating with a former member, then he should be held liable if his actions can be shown to interfere with the rights of others.