Although the academic year has just come to end, the argument over Yale’s decision not to hire University of Michigan Professor Juan Cole is just beginning. And it is moving rapidly beyond the question of Mr. Cole himself to the question of academic freedom and how Yale itself is navigating the political seas.

In the fall, when Yale undertook a search for a professor of modern Middle East studies, Mr. Cole, a former president of the Middle East Studies Association, quickly made the search committee’s short list. As the search committee’s top choice, Mr. Cole needed the approval of the history and sociology departments, with whom he would have been associated if he joined the faculty, and of Yale’s Senior Appointments Committee. Mr. Cole secured the backing of the two faculty departments, but was voted down by the Senior Appointments Committee.

Yale’s consideration of Mr. Cole sparked considerable debate among pundits and academics alike. Articles calling attention to Mr. Cole’s most egregious statements appeared in newspapers from the Yale Daily News to the Wall Street Journal. In the pages of this newspaper, I opposed Mr. Cole’s appointment on the grounds of his well-documented hostility to Israel, statements on his blog, which is called Informed Comment, and his scholarship on the modern Middle East, which exhibits the crude polemics that characterize his blog.

The way Mr. Cole articulates his opposition to Israel’s Likud party provides a glimpse into his views. The “real roots” of the party, he argues, lie in a “kind of fascism”; the party itself “isn’t morally superior in most respects to the Syrian Baath … it treats at least 3 million people no better than and possibly worse than the Syrian Baath treats its 17 million.” As for Jewish American public servants, he contends that “Jewish American Likudniks” use the Pentagon as “Israel’s Gurkha regiment, fighting elective wars on behalf of Tel Aviv.”

Since the Power Line blog broke, on June 2, the news of Yale’s decision to take a pass on Mr. Cole, the saga has quickly turned into a debate about whether Yale’s action constitutes politically motivated “blackballing” with overtones of McCarthyism. Mr. Cole himself peddles this charge; he told the Jewish Week newspaper that “the concerted press campaign by neoconservatives against me … was inappropriate and a threat to academic integrity.” (Apparently the professor considers the exercise of free speech among his detractors “inappropriate.”) In an article titled “Blackballed at Yale,” Inside Higher Ed quotes a New York University professor, Zachary Lockman, to the effect that press criticism of Mr. Cole as well as Yale’s decision not to hire him constituted “an assault on academic freedom and the academic enterprise.”

The assertion that Yale’s decision is a denial of academic freedom is a stretch by even the most liberal standards. Yale’s decision, made by academics, was an exercise in academic freedom. And it hardly removes his ability to voice his views. Mr. Cole has spoken freely in public and on his blog in the past several years and will, he assured Inside Higher Ed, “redouble my efforts. Attempts at blackballing and at making intellectuals taboo always demonstrate the fear of opponents.”

A number of Mr. Cole’s defenders argue that his statements outside the classroom should have played no role in Yale’s decision. It’s hard to ascertain whether they did, but certainly Mr. Cole’s critics have focused less on the substance of his scholarship than on his polemics. The members of the Senior Appointments Committee may not have been impressed by the fact that Mr. Cole tends decorously to avoid making hostile remarks inside the classroom and to limit his vulgarities to his Web site. But he does express himself there in a most unprofessorial way. Washington Times columnist Joel Mowbray called attention to Mr. Cole’s declaration that “We don’t give a rat’s a** what Ahmadinejad thinks about European history or what pissant speech the little s**t gives.”

It goes without saying that in the academic world, one’s public behavior affects one’s relationships with his students, peers, and the university with which he is associated. To chalk up Mr. Cole’s vituperation to a mere difference in political coloration that lies outside the realm of professional concern, as his opponents would have us do, would be to turn a blind eye to his beliefs and the manner in which he has chosen to express them.

This is an important moment for Yale and, given Yale’s great stature, the American academy. The past few years have seen Columbia embroiled in a major scandal over its Middle Eastern studies and, most recently, the decision of a Harvard dean, Stephen Walt, to attack the American pro-Israel community. While Yale’s committee isn’t speaking, we can hope that, with Yale’s decision over its Taliban-spokesman-turned-student pending, it has decided it doesn’t want to go down the same road. If so, it will prove a wise decision in the long run.

Ms. Johnson graduated from Yale in May.