By most measures, Holden Thorp’s five-year tenure as the chancellor of the University of North Carolina at Chapel Hill, which is coming to an end next month, was a roaring success. The university went from 19th to 9th in federal research grants. Undergraduate applications rose 43 percent. And, at a time when university budgets are under extreme pressure, Thorp helped keep U.N.C. an affordable public university.

But you won’t find a lot of people giving Thorp, 48, a pat on the back. For the last three years, North Carolina was mired in an athletic scandal. And the fact that it took place on Thorp’s watch overshadows everything else he did.

Though it started out as an N.C.A.A. rules-violation investigation, it morphed into an academic scandal when it was discovered that the chairman of the African and Afro-American Studies Department had long allowed students — athletes very much included — to take no-show classes.

For a university that had long held itself out as one of the “good schools” athletically, the scandal has been humiliating. The N.C.A.A. meted out penalties to the football team. The football coach, Butch Davis, was fired. The athletic director resigned. Even the college accrediting agency got involved.

By his own admission, Thorp was shellshocked by the experience of dealing with the scandal. As a lifelong North Carolina partisan, he had bought into the myth of the university as a place that harvested genuine student-athletes. The scandal showed him a reality he never before had to face.

It also engulfed him. If you are a college chancellor or president, you can’t delegate when there is a problem in the athletic department. “The governing board, the newspaper, the fans, the faculty, they all expect you to sort it out,” he said. He was spending, literally, half his time dealing with the football team. Yet he had no real experience with the business of college athletics — nor, for that matter, do most college presidents.

He found himself buffeted this way and that. At first, he supported his coach, but then he finally felt he had to fire him. He did so at the worst possible moment: on the eve of a new season. His press conferences dealing with the scandal were, by his own admission, “terrible.” He was, to be blunt, in over his head.

And as he departs U.N.C., his message is that virtually all college presidents are in over their heads when it comes to their athletic departments. They have no background, no experience, that would prepare them for overseeing the $6 billion entertainment complex that big-time college sports has become. In he early 1990s, the Knight Commission on Intercollegiate Athletics issued a series of reports saying that college presidents needed to regain control of their athletic departments and restore “integrity.” The N.C.A.A. adopted this position.

But today, notwithstanding this supposed reform, the system is as morally corrupt as ever — and far more awash in money. It’s conference presidents, not college presidents and chancellors, who run college sports. The prototypical modern athletic director is David Brandon at the University of Michigan. His previous job — are you sitting down? — was chairman and chief executive of Domino’s Pizza. He is an unabashed revenue maximizer. Compared with the hard-nosed businessmen who control college sports, the presidents and chancellors are babes in the woods. The main thing they offer everyone else in the system is cover.

Not surprisingly, Thorp’s comments have not exactly been embraced. At U.N.C., there is still a lot of indignation, some deserved, at the way Thorp handled the scandal. Some people think he is trying to shuck his responsibility.

People associated with the Knight commission are also upset. Hodding Carter III, a former president of the Knight Foundation, which finances the commission, was quoted as saying that Thorp was “wrong on every count.” But he’s not. Even the Knight commission has begun to examine whether the system is so broken that it can’t be reformed.

That is what Thorp now thinks. He is not ready to go as far as I do, namely, end the hypocrisy and start calling “student-athletes” what they really are: employees who deserve to earn a paycheck for their labors. But he does believe athletes should be allowed to attend school after their playing days are over. And, he said, “the concept of amateurism” — the current bedrock of college athletics — “needs to be examined.” For a college chancellor, those are radical words.

Thorp himself will soon move to Washington University in St. Louis, a first-rate academic institution that no one will ever mistake for the University of North Carolina athletically. It is in Division III, meaning, among other things, it doesn’t offer athletic scholarships.

Not long ago, when he was being taken around the Washington University campus, Thorp remarked, “I hear that the football stadium seats 3,500.”“Yes,” came the response, “but it’s never been tested.”“I’m looking forward to Division III,” Thorp told me.