It seems to be the case that Stallman did engage in inappropriate behavior - which perhaps should have been dealt with differently by CSAIL, MIT, the FSF board etc. The appropriate response may very well have been to ask for his resignation.
But those behaviors are not why he was asked to resign. Reference to his past behavior was a post-hoc rationalization. It seems the real reason he was fired was because he expressed a difference of opinion over the nature of Marvin Minksy's guilt as a result of his association with Epstein.
Well, it wasn't even about the opinion he expressed, rather he was fired because someone publicly misinterpreted his opinion, and that mistaken opinion was picked up by the media.
Well, it wasn't even about the misinterpreted opinion. He was fired because MIT is (I'm sure) facing some very serious scrutiny over it's entanglements with Epstein, and the very real concern that one of it's famed professors may have been a co-conspirator in a powerful and depraved criminal ring. The whole Stallman affair serves as a nice deflection from that scrutiny.
As it stands, it does not even look like Minsky ever participated in said criminal activity (as far as I can tell, the victim only said that she was compelled to offer herself to Minsky, and another witness claimed that Minksy turned her down). While there likely were many powerful people who were knowing participants in Epstein's activities, it seems that Epstein was also someone who liked to befriend very smart STEM folks, and not all of them may have been aware as to what exactly Epstein was involved in.