The Department of Defense has begun a crackdown on how Islam is taught to the U.S. military. Reacting to press reports indicating a serious problem, Shairman of the Joint Chiefs of Staff General Martin Dempsey has ordered a thorough scrub of how DoD talks about Islam to its personnel. The directive requires an immediate end to inflammatory rhetoric about a “war on Islam” inside the Department, particularly within the Professional Military Education (PME) establishment.

The only surprise to anyone who has been close to this issue is that it took a decade to reach this point. It’s hardly been a secret that, in the aftermath of 9/11, as DoD scrambled to make sense of what motivated al-Qaeda and its sympathizers, the Pentagon opted for a quantity-over-quality approach. While DoD has engaged many serious scholars on Islam and Islamist militancy, it has also relied on people much less informed. At best, some have engaged in overgeneralizations and bad analogies; at worse, some are charlatans with a barely concealed agenda. PME has hosted many talented speakers with real background in the subject who have broadened minds, but my institution, too, has brought in speakers who are now the subject of controversy.

The instant-Islam-experts have been cashing in for more than a decade, and some of them have virtually no credentials other than an obviously strong dislike of Islam (and an equally strong desire to get paid). One need not agree with the assertion that the enemy is "manufactured" to find much of what DoD, and more broadly the U.S. government, has been doing in this arena to be questionable and in need of just the sort of deep review that Chairman Dempsey has now mandated.

American taxpayers, as well as our many Muslim allies in the struggle against al-Qaeda and its followers—who have lost many more lives in this fight than Americans have—are entitled to wonder the purpose of lectures, conducted at PME institutions by serving military officers, calling for Hiroshima-style solutions to the “problem” of Islam. It cannot comfort any sensible citizen to know that related thinking, pointing at Islam and not al-Qaeda as the “real” enemy, has been provided to the FBI, too.

Thanks is due to Wired magazine for bringing such incidents, which can no longer be termed isolated, to light. What is most disturbing is that, in nearly every case of Islam-is-the-enemy thinking being taught to our military and law-enforcement personnel, the instruction has been given by individuals without serious background in the subject; in more than a few cases, they are lacking any related scholarly grounding whatsoever. What they do possess, however, is a certainty that they are in the right and that unnamed persons are preventing “the truth” from coming out. It hardly needs to be said that, at nearly every point, such governmentally provided lecturers are deeply at odds with the stated policies of both the Bush and Obama administrations. I have had the distinct displeasure, many times, of witnessing speakers at DoD events explain to the audience that we indeed really are at war with Islam; more than once, these “experts” were basing their opinions on having been Christian missionaries.

In hindsight, it’s not difficult to discern how DoD got into this predicament. One cause is surely the simplistic, even Manichean vision that was perhaps forgivable a decade ago but is not so now. Also important is what might be termed the “Israelization” of U.S. security thinking since 9/11, at least in certain quarters. There has always been more than a little admiration for Israel in the U.S. military, a wish that America could be as forward-leaning as Israel about terrorism, an unspoken desire to live in the world of en brera (“no choice”), where hard men get to do difficult things with the full, even unquestioned support of the national leadership. In that sense, the United States has become more like Israel since 2001, but it bears asking how much the global hegemon helps itself by acting in a devil-may-care fashion—or like a small, outnumbered state that really is surrounded by hostile forces.

More than a decade into the struggle against al-Qaeda and its allies, it is time to show maturity and wisdom. Let it be said that part of the maturity that is required means not simply expelling discussion of Islam from teaching about terrorism in PME. Al-Qaeda is nothing if not a very successful “faith-based initiative,” and its motives and strategy cannot be understood without reference to the religion that guides literally everything it does—even if the al-Qaeda vision is one very foreign to most Muslims and indeed repellant to many of them.

Given the common DoD tendency to overkill, the Pentagon must be careful not to stifle discussion. The issue of political Islam—not just terrorism—will not go away and must be subject to legitimate and learned inquiry and debate inside the U.S. government. Whether the Muslim Brotherhood can assimilate to post-modern Western democratic norms remains a very open question, and it is certainly true that some of its front organizations have supported what can be fairly termed subversion against the American system.

Senator Joe McCarthy did more damage to legitimate anticommunism in America than anything the Soviet apparat was capable of pulling off. Just as with McCarthy, let us not allow charlatans to derail scholarly inquiry and discussion. There really was a vast Soviet-agent network in the United States in the 1940s—one aimed at subversion, espionage and terrorism—just as there really is a global Islamist extremist network today. Let’s clean house, as respectable and decent anticommunists did in 1954 with McCarthy, and get back to the serious business of understanding why al-Qaeda does what it does.

John R. Schindler is professor of national-security affairs at the U.S. Naval War College and a former expert in counterterrorism with the National Security Agency. The opinions expressed here are entirely his own.