Fish notes that courts generally seek to avoid the inherent conflict between two cherished ideals in Western Liberal Society by reducing the question to matters of procedure and forum. As Fish observes, the law has essentially eliminated an earlier interpretation of the Establishment Clause that required an utter prohibition on state subsidy to religious institutions by transforming religious expression into simply one more viewpoint. At the same time, however, the court removed any special status of religion with regard to secular law so that a neutral law not designed to prohibit "free exercise," but having that effect, must be obeyed. Thus, native American or Rastiffarian practitioners may not use peyote or marijuana in religious rituals. And nor, in this case, can the Christian Legal Society demand an exemption from a state school's policy of requiring non-discriminatory admission for all recognized student organizations.
The article primarily explores the tensions, rather than advocating a particular point of view. Fish's sympathy is with CLS (it was comments on an earlier column that prompted this response). As a religious lawyer who has looked at the same tensions in other contexts, I think the author does as good a job as one can trying to examine the underlying tensions in the law and society objectively. It is, however, a difficult issue to approach purely objectively, without regard to the underlying outcomes.
As with many such irresolvable conflicts, I have no problem in saying that we simply as a society end up resolving this one way or another based on a best guess and arbitrary moral judgments. I sadly find myself in agreement with Employment Div. v. Smith, the case that subordinates the Free Exercise clause to neutral laws that happen to prohibit free exercise of religion, because I cannot see any limiting principle to the alternative. (I say "sadly" because the movements to outlaw shchitah (kosher ritual slaughtering) and circumcision place core religious practices of my own at risk.) I draw comfort in cases such as CLS in the idea that, even with reducing religion to merely a point of view, such groups still have the right to express their views and control their message and venue. CLS may not be able to exclude active homosexuals. But the school cannot stop CLS from holding meetings where members express the view that homosexuality is a choice and contrary to God's will, or from removing members who are actively disruptive, any more than the school can prevent the GLBT organization from expressing the view religions which hold that God hates homosexuality are merely expressions of human bigotry -- and removing members of such religions who seek to disrupt these expressions by arguing the opposite case. It is rather reminiscent of Queen Elizabeth's approach to religion: "Just shut up, show up on Sunday, and read out of the Church of England miscellany and no one will worry whether you really believe it."
To conclude, I like Fish's essay and recommend it. Whichever way one comes out in the tension between various ideals, it is important to recognize it is a tension and that it will invariably lead to less than perfect results. I am willing to ban things such as suttee (widow burning) even while recognizing that doing so violates a long-standing religious custom while trying to accommodate other religious needs on purely utilitarian grounds, without trying to pretend that suttee is any more or less a religious ritual sincerely held by its adherents. I could wish it were possible in a wide variety of debates to be able to say "yes, sorry, but life is a sliding scale when trying to work out a system of 300 million people living together and your core belief just got run over by a competing core belief." Unfortunately, most people seem to require the additional element of de-legitimizing the opposition to console themselves.