A recent blizzard of liberal columns has framed the debate over American Islam as if it were no more than the most recent stage in the glorious history of our religious tolerance. This phrasing of the question has the (presumably intentional) effect of marginalizing doubts and of lumping any doubters with the anti-Catholic Know-Nothings, the anti-Semites, and other bigots and shellbacks. So I pause to take part in a thought experiment, and to ask myself: Am I in favor of the untrammeled “free exercise of religion”?

No, I am not. Take an example close at hand, the absurdly named Church of Jesus Christ of Latter-day Saints. More usually known as the Mormon church, it can boast Glenn Beck as one of its recruits. He has recently won much cheap publicity for scheduling a rally on the anniversary of Martin Luther King Jr.’s March on Washington. But on the day on which the original rally occurred in 1963, the Mormon church had not yet gotten around to recognizing black people as fully human or as eligible for full membership. (Its leadership subsequently underwent a “revelation” allowing a change on this point, but not until after the passage of the Civil Rights Act.) This opportunism closely shadowed an earlier adjustment of Mormon dogma, abandoning its historic and violent attachment to polygamy. Without that doctrinal change, the state of Utah was firmly told that it could not be part of the Union. More recently, Gov. Mitt Romney had to assure voters that he did not regard the prophet, or head of the Mormon church, as having ultimate moral and spiritual authority on all matters. Nothing, he swore, could override the U.S. Constitution. Thus, to the extent that we view latter-day saints as acceptable, and agree to overlook their other quaint and weird beliefs, it is to the extent that we have decidedly limited them in the free exercise of their religion.

One could cite some other examples, such as those Christian sects that disapprove of the practice of medicine. Their adult members are generally allowed to die while uttering religious incantations and waving away the physician, but, in many states, if they apply this faith to their children—a crucial element in the “free exercise” of religion—they can be taken straight to court. Not only that, they can find themselves subject to general disapproval and condemnation.

It was probably the latter consideration that helped impel the majority of American Orthodox Jews to give up the practice of metzitzah b’peh, a radical form of male circumcision that is topped off, if you will forgive the expression, by the sucking of the infant’s penis by the rabbi or mohel so as to remove any remaining blood or debris. A few tiny sects still cling to this disgusting ritual, which in New York a few years ago led to a small but deadly outbreak of herpes among recently circumcised babies. On that occasion, despite calls for a ban on the practice from many Jewish doctors, the vastly overrated Mayor Michael Bloomberg chose an election year to say that such “free exercise” should not be interfered with.

We talk now as if it was ridiculous ever to suspect Roman Catholics of anything but the highest motives, yet by the time John F. Kennedy was breaking the unspoken taboo on the election of a Catholic as president, the Vatican had just begun to consider making public atonement for centuries of Jew-hatred and a more recent sympathy for fascism. Even today, many lay Catholics are appalled at the Vatican’s protection of men who are sought for questioning in one of the gravest of all crimes: the organized rape of children. It is generally agreed that the church’s behavior and autonomy need to be modified to take account both of American law and American moral outrage. So much for the naive invocation of “free exercise.”

One could easily go on. The Church of Scientology, the Unification Church of Sun Myung Moon, and the Ku Klux Klan are all faith-based organizations and are all entitled to the protections of the First Amendment. But they are also all subject to a complex of statutes governing tax-exemption, fraud, racism, and violence, to the point where “free exercise” in the third case has—by means of federal law enforcement and stern public disapproval—been reduced to a vestige of its former self.

Now to Islam. It is, first, a religion that makes very large claims for itself, purporting to be the last and final word of God and expressing an ambition to become the world’s only religion. Some of its adherents follow or advocate the practice of plural marriage, forced marriage, female circumcision, compulsory veiling of women, and censorship of non-Muslim magazines and media. Islam’s teachings generally exhibit suspicion of the very idea of church-state separation. Other teachings, depending on context, can be held to exhibit a very strong dislike of other religions, as well as of heretical forms of Islam. Muslims in America, including members of the armed forces, have already been found willing to respond to orders issued by foreign terrorist organizations. Most disturbingly, no authority within the faith appears to have the power to rule decisively that such practices, or such teachings, or such actions, are definitely and utterly in conflict with the precepts of the religion itself.

Reactions from even “moderate” Muslims to criticism are not uniformly reassuring. “Some of what people are saying in this mosque controversy is very similar to what German media was saying about Jews in the 1920s and 1930s,” Imam Abdullah Antepli, Muslim chaplain at Duke University, told the New York Times. Yes, we all recall the Jewish suicide bombers of that period, as we recall the Jewish yells for holy war, the Jewish demands for the veiling of women and the stoning of homosexuals, and the Jewish burning of newspapers that published cartoons they did not like. What is needed from the supporters of this very confident faith is more self-criticism and less self-pity and self-righteousness.

Those who wish that there would be no mosques in America have already lost the argument: Globalization, no less than the promise of American liberty, mandates that the United States will have a Muslim population of some size. The only question, then, is what kind, or rather kinds, of Islam it will follow. There’s an excellent chance of a healthy pluralist outcome, but it’s very unlikely that this can happen unless, as with their predecessors on these shores, Muslims are compelled to abandon certain presumptions that are exclusive to themselves. The taming and domestication of religion is one of the unceasing chores of civilization. Those who pretend that we can skip this stage in the present case are deluding themselves and asking for trouble not just in the future but in the immediate present.

Like Slate on Facebook. Follow Slateand the Slate Foreign Desk on Twitter.