A long-awaited independent report on MIT’s role in the federal prosecution of Aaron Swartz concludes that the institution behaved neutrally throughout the affair, but “did not duly take into account the wider background of information policy against which the prosecution played out and in which MIT people have traditionally been passionate leaders.”

The 180-page report prepared by MIT Professor Hal Abelson was requested by the university’s president, L. Rafael Reif, in early January, after Swartz, 26, took his own life. Swartz was facing a looming trial on federal hacking and wire fraud charges for using MITs public network to download 4 million academic papers from the JSTOR clearinghouse.

MIT faced a firestorm of criticism in the wake of Swartz’s suicide. Critics, including Swartz’s family and prominent MIT alumni, said the institution betrayed its own principals by not advocating for less harsh treatment of Swartz, who potentially faced seven years in prison if convicted at trial. Swartz rejected plea bargains of between four and six months in custody that would still have left him with a lifelong felony record.

Reif, in an open letter today, said MIT was vindicated by the report. “The report also sets the record straight by dispelling widely circulated myths,” wrote Reif. “For example, it makes clear that MIT did not ‘target’ Aaron Swartz, we did not seek federal prosecution, punishment or jail time, and we did not oppose a plea bargain.”

But Robert Swartz, Aaron Swartz’s father, says the finding “makes clear that MIT’s role is central in this tragedy.” And Taren Stinebrickner-Kauffman, Swartz’s partner, had strong words about the report. “MIT’s behavior throughout the case was reprehensible,” she wrote in a blog post, “and this report is quite frankly a whitewash.”

JSTOR began complaining to MIT in September 2010 that someone was taking advantage of MIT’s subscription to the academic archive to aggressively bulk-download articles. The downloading continued sporadically until early January 2011, when MIT traced the activity to an unlocked network closet in the basement of Building 16, where someone — later determined to be Swartz — had secreted a laptop computer wired to the university’s public network.

MIT police called the Cambridge police, who showed up with a Secret Service agent from the New England Electronic Crimes Task Force — sparking the federal investigation.

The report says that MIT officially adopted a neutral posture with respect to the federal criminal case, treating it as an outside matter. But it also details extensive cooperation between MIT officials and federal agents and prosecutors.

MIT sniffed network traffic from Swartz’s computer and provided logs voluntarily to the government, without demanding a subpoena. And MIT did not offer to give Swartz’s defense team access to the employees interviewed by prosecutors. “The choice not to do this was based on a judgment that the criminal process was sufficiently fair, without the need for it to provide equality of outcome,” the report notes.

“The report makes clear that MIT was not neutral,” says Robert Swartz, who’d met with MIT repeatedly during the prosecution to plead for his son. “But they should not have been neutral. They should have advocated of Aaron’s behalf, because the law under which he was charged was wrong.”

“They cooperated with prosecutors in endless ways, and they were fundamentally opaque to us.”

In all, MIT comes across as handling the prosecution the way most any large company would. It neither drove the case, nor demanded any particular outcome or sentence. But despite its position of “neutrality,” MIT cooperated much more closely with the prosecution than with the defense.

The report also notes that the widespread concern that trailed Swartz’s suicide was hard to find while he was still alive and fighting the case.

[T]here were very few direct contacts made with the MIT administration to encourage a change on the part of MIT from neutrality to advocacy. MIT’s student newspaper, The Tech, reported regularly on the progress of the case, but this did not prompt any editorials or opinion pieces before Aaron Swartz’s suicide. Nor did people who later criticized MIT for not advocating for Aaron Swartz approach the MIT administration making the case for MIT to advocate for him before the suicide.

Abelson and his panel interviewed 50 people and reviewed 10,000 pages of documents to produce the report, about 3,000 of which were released in redacted form today.

Separately, MIT and JSTOR are moving to intervene in a FOIA lawsuit filed by this reporter against the Department of Homeland Security seeking the release of Swartz’s 8,000-page Secret Service file. MIT and JSTOR are arguing for the right to review the documents first and make their own redactions, on top of the redactions made by the government. I’m opposing their intervention. They’re scheduled to file additional briefs on their position today.

The full MIT report follows.

Disclosure: I knew Swartz and worked with him on a project.