The computer scientist Richard Stallman has resigned from MIT and the Free Software Foundation (FSF), which he founded and led, after leaked emails appeared to show him downplaying another academic’s alleged participation in the purported sex trafficking of minors by Jeffrey Epstein.

On his personal website, Stallman wrote: “I am resigning effective immediately from my position in [the Computer Science and Artificial Intelligence Laboratory, or CSail] at MIT. I am doing this due to pressure on MIT and me over a series of misunderstandings and mischaracterizations.”

The FSF announced Stallman’s resignation as president and from its board of directors.

MIT was already at the center of the Epstein storm, in the wake of revelations that its Media Lab accepted $7.5m in funding from the disgraced financier or a group of donors connected to him. Media lab director Joi Ito resigned.

Stallman’s emails came to light after an MIT graduate, Selam Jie Gano, published a Medium post calling for his removal.

According to the Medium post, Stallman wrote in response to a student’s message about an event protesting the acceptance of Epstein’s money. The emails, which were published by Vice were sent to a CSail mailing list.

Referring to Epstein accuser Virginia Giuffre, who alleged in court papers she was sent to have sex with the late MIT cognitive scientist Marvin Minsky, Stallman wrote: “We can imagine many scenarios, but the most plausible scenario is that she presented herself to him as entirely willing.

“Assuming she was being coerced by Epstein, he would have had every reason to tell her to conceal that from most of his associates.”

When a student on the email thread noted that Giuffre was allegedly forced into sex at 17, Stallman responded: “It is morally absurd to define ‘rape’ in a way that depends on minor details such as which country it was in or whether the victim was 18 years old or 17.”

Stallman added: “All I know [Giuffre] said about Minsky is that Epstein directed her to have sex with Minsky. That does not say whether Minsky knew that she was coerced.

“We know that Giuffre was being coerced into sex – by Epstein. She was being harmed. But the details do affect whether, and to what extent, Minsky was responsible for that.”

Minsky died in 2016, aged 88.

Stallman, 66, has contributed to the Guardian. On Monday he posted a statement to his website before his resignations were made public. Reports about his views on Epstein were “misleading”, he said.

“The coverage totally mischaracterised my statement. Headlines say that I defended Epstein. Nothing could be further from the truth.

“I’ve called him a ‘serial rapist’, and said he deserved to be imprisoned. But many people now believe I defended him – and other inaccurate claims – and feel a real hurt because of what they believe I said.

“I’m sorry for that hurt. I wish I could have prevented the misunderstanding.”

On Monday MIT Media Lab academic Neri Oxman apologised for “having received funds from Epstein, and deeply apologize to my students for their inadvertent involvement in this mess”.

In a statement to magazine Dezeen, Oxman said she had been told to keep the $125,000 2015 donation confidential, “so as not to enhance [Epstein’s] reputation by association with MIT”.

Harvard received $9m from Epstein prior to his 2008 guilty plea to state-level prostitution charges in Florida.

Epstein, a registered sex offender, killed himself in jail last month while awaiting federal sex trafficking charge.

Prosecutors alleged that some of his victims were as young as 14.