1. He only has honorary doctorates. If you wouldn't say "Dr. Zuckerberg," don't say "Dr. Stallman." (Meanwhile, Dr. Bill Cosby has an earned doctorate!)
2. Related to the previous point, his "position" at MIT was an office with a mattress, thanks to having influential friends in the faculty there. He was not paid by MIT, he had no teaching role at MIT, and he was part of no MIT research projects.
3. Even if every error printed by the media was corrected, there is - and has been for years - significant dissatisfaction with him at MIT, within the FSF, within the GNU Project, and within the free software community at large.
4. Stallman continues to be welcome to debate the truth. It's a valuable part of a free society. What MIT and the free software community has made clear is that he is not welcome to debate the truth and serve as a representative of MIT and of the free software community. MIT gained nothing direct from his affiliation as unpaid research staff assigned to no research projects; all they gained was an association with his reputation. As soon as that becomes a negative association, there's no rational reason to keep it. Similarly, the free software community has argued for the removal of Stallman from his leadership position because they've seen that he prioritizes his interest in debating about sexual norms over his interest in leading and growing the free software community. (See, for instance, http://ebb.org/bkuhn/blog/2019/10/15/fsf-rms.html .)
It is true that the media flare-up about Stallman's Minsky/Epstein commentary was the immediate political motivation for him leaving his MIT affiliation (since the most active benefit of his affiliation was his presence on the CSAIL general mailing list where he made this comments, and there has been general displeasure at his presence there for well over a decade) and his FSF role. But I'm not sure what the benefit to the world is to re-appoint him to his FSF role only to "re-try" him for his actual failure to do his work - especially when so many GNU projects seem on the verge of forking.