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After the scandal broke, admin­istrators suggested the process would conclude in the early part of the semester, while resident deans were told to ­advise student athletes to consider withdrawing.

Some did. Others held out, taking the risk of staying in school in the hope that they would be exonerated or that if they were found guilty, they would find out while much of their semester’s tuition could be prorated and recouped.

It was a stressful process for students. Like clockwork every Tuesday night, another flurry of decisions was handed out and more students would suddenly disappear from classes and team practices.

The magnitude of the inquiry meant that students appeared before a subcommittee of three members of the Administrative Board. Students said they never had the chance to appear before the full board, which voted on their cases.

Others criticized what they say is the conflict of interest in the role played by resident deans.

Most of the time, these deans, members of the faculty, serve as academic advisers. But in Administrative Board investigations, their conversations are not privileged; share a damning detail with your dean, and the rest of the board will probably know.

“It’s almost unfair not to have a lawyer in the room,” said a student who was eventually exonerated. “These are Harvard professors, incredibly smart people. They know what they’re doing. It’s not supposed to be adversarial, but it felt very ­adversarial.”

Harvard has also taken heat from its alumni community. In a letter to president Drew Faust this month, Harvard graduate Thomas G. Stemberg, cofounder of Staples and a prominent fund-raiser for the college’s basket­ball program, lambasted the university’s response.

“How can one come to any conclusion other than the university has a bloated bureaucracy so intent on being politically correct that its students and its mission are forgotten?” wrote Stemberg.

Former Harvard College dean Harry Lewis said he wished the episode had prompted more soul-searching within the university on the value of take-home exams. Administrators should have used more discretion, he said, because of “the mismanagement of the course.”

“I’m certainly not suggesting that Harvard should have walked away from people who did a cut-and-paste job and turned in lots of verbatim text,” Lewis said. “But it seems that a lot of the cases were much more complicated and much grayer.”

Other Ivy League schools have handled such large-scale allegations more circumspectly.

In 2000, Dartmouth College accused 78 students of cheating in a computer science class. Some had found homework ­answers on the class’s online web server, accidentally left unprotected by a password. Others received the answers from teaching fellows who thought they had the professor’s permission to discuss solutions.

James Larimore, dean of Darmouth at the time, said the school’s disciplinary board conducted extensive investigations before deciding to drop the charges for fear of unfairly punishing some students.

“Ultimately . . . the committee was frustrated by its inability to determine with reasonable confidence which individuals had cheated and to reliably distinguish students who had ­engaged in academic dishonesty from classmates who had sought and used help that they assumed was appropriate,” ­Larimore said.

The similarities, Lewis said, are striking.

“Harvard probably should have done what ­Dartmouth did,” he said.

Martine Powers can be reached at mpowers@globe.com or on Twitter @martinepowers.