He was asked to resign because it's a good play for MIT, you don't have to defend against a wrongful termination suit if the person in question willingly resigns.
If he wanted to defend himself, he would have stayed and fought, let himself get fired, file a lawsuit.
But he resigned, willingly.
Or possibly, because both the SFC [1] and the head of the GNOME foundation [2] said that they would find it unacceptable to work with the FSF as long as Stallman was still the leader, he realized there was no way staying on would be possible.
[1] https://sfconservancy.org/news/2019/sep/16/rms-does-not-spea... [2] https://blog.halon.org.uk/2019/09/gnome-foundation-relations...
Clearly, as the angry Twitter mob of virtue signalers clearly has no desire or respect for objective arguments and accusations based on facts, let alone what the law actually says.
This smear campaign targeted at Stallman only ceased to be about the law once the self-righteous Twitter mob of virtue signallers was forced to admit that Stallman was in fact absolutely right to point out that the accusations correspond to statutory rape instead of sexual assault.
Unfortunately instead of doing the honest thing and admit they were wrong, they started moving the goal post and resort to Cardinal Richelieu tactics to try to come up with anything to keep up with the harassment and persecution.
And surely to defend a rapist, even an accused one, is nearly as bad as being a rapist? Why, perhaps we should skip the courts all together and simply tar and feather them in the public. That's worked out well historically...