What I do want to address are some of the ideas expressed in the column. Specifically the tendency to attribute beliefs that aren't easily reconciled with the liberal state to either religions, Christians, or religious organizations, instead of attributing them more narrowly to groups that specifically express these beliefs (though to be fair he makes the distinction clear in places and very distinctly so in the original column). The problem with this is that it sets up a tension between religious belief and reason, a tension that is well expressed in the following quotes (note the broad contrast being drawn between the liberal state and religion in the opening sentence):
What it goes to show is that the conflict between the liberal state, with its devotion to procedural rather than substantive norms, and religion, which is all substance from its doctrines to its procedures, is intractable. In his “Political Liberalism,” John Rawls asks how democracy’s aspiration for “a just and stable society of free and equal citizens” can be squared with the fact that some of those citizens hold beliefs that are exclusionary; how can they receive equal treatment if they deny it to others?
Another philosopher, Thomas Nagel, explains what must happen if the liberal state and its religious members are to co-exist in harmony: “Liberalism should provide the devout with a reason for tolerance,” that is, with a reason for putting tolerance above commitment to an absolute and demanding truth. There are no such reasons; the devout can only recognize reasons that flow from the structure of their devotion; liberalism can only give reasons that reflect its own commitment to neutrality. The rapprochements between them are fitful and temporary products of the endless political maneuverings we see in this case and in every case brought under the religion clause. That’s just the way it is and always will be.
This framing draws a sharper distinction between religious belief and the normative beliefs of the liberal state than I believe are accurate. I am certain that Dr. Fish is aware of these distinctions but with a subject that is often this emotional I believe it is very important to be explicit about distinctions to avoid the presentation of an inherent opposition between reason and religion that is characteristic of so much modern discourse. Reconciling religion with the above notions of the liberal state is rather important to me; I tend to think that at the very heart of the transition to modernity is a shift from prescriptive ideas about how people should act to procedural notions which lets us stop worrying about things we can't change and get on with progress. A vast over-simplification, but in all the reading I do on the subject the one thing that stands out is a profound intellectual shift; to me this debate is about whether we as a society want to be modern or if we want to go back to a belief system incapable of seeing the world in terms that allow for fundamental change and progress that would condemn us to reaching the kind of poor, bleak, unchanging equilibrium that characterized all history before modern times.
Back on topic from that brief digression. The description of religion given seems to only fit more traditional or fundamentalist interpretations of religious belief, it does not seem descriptive of more liberal traditions. Thinkers since the Enlightenment, and really from ever since scholarly studies started seeing discrepancies between different versions of the Bible, have often reached their own conclusions about the faith that are perfectly consistent with the liberal state. Some of the beliefs most difficult to reconcile with the modern liberal state aren't even universal to earlier Christian traditions, much less modern interpretations; many of the beliefs most difficult to reconcile with modern ideas about the liberal state are founded on an Augustinian interpretation of Christianity that was not accepted outside the west. At the very simplest, it just was never that big of a jump to reject the Augustinian notion of a fallen world and conclude that since the Bible has changed over time that the world itself is the most accurate expression of God's will with the Bible being the most valuable guide to interpreting a vastly confusing world, though not one that should take precedence over actual observation of the world.
Of course, go down this road too far and you've left Christianity and become a deist (a journey I'll confess I've made myself) but any history that looks at religion has to confront that ever since the Enlightenment plenty of people that consider themselves to be religious have made this jump. A disservice is being done to exploring the relation between the liberal state and religion in general when a distinction is not made between religious beliefs that have no problem reconciling themselves with the liberal state and those that do. There simply isn't a sharp line that can be drawn between religion and reason, out of the Enlightenment a kind of faith grew that offered a completely viable third path.
Though at the end of all this I do realize I haven't addressed the central conundrum of what to do in a liberal society where some have exclusionary beliefs. I do think realizing that this does not describe everyone who falls under terms such as religious, Christian, or religious organization (though I do think liberal versions of religion seem much less organized, this is likely due to the fact that most emphasize a personal version of faith over the organized expression, which leaves the less liberal variants the ones with the strongest voice in public discourse) is an essential distinction to make.
[Edited for grammer, further edits are entirely possible if I catch more errors.]