I concur with your thinking on this. I'm no fan of Stallman, and I think both the FSF and CSAIL are probably better of without him ghosting around, but the way in which this happened is deeply problematic. Stallman's opinion in this case was clearly a bit out of whack, but the tone and style of the message was completely on point for his character. And therein lies the problem here, I'm fairly sure Stallman's points could have been formulated in a way that would not have provoked such a visceral reaction. Stallman tends to be unable to empathize with his interlocutors (or at least unable to express such empathy in writing), turns everything that happens into a case study in moral philosophy, and is a bit terse and snippy in his emails. All that makes him not a pleasant debater for sure, but are we as a society really willing to take somebody's livelihood because of their poor rhetoric style?
The next thing that happened was that the news picked it up, but got most of the details wrong, taking the problematic statement out of context, mischaracterizing his relationship with MIT, mischaracterizing what he did exactly, etc and as a result whipping up an angry mob demanding his firing.
Now, of course many people have wanted Stallman gone for all sorts of reasons of his general unpleasantness for many years, so this seems to have been as much a convenient excuse to rally those efforts as anything else. Nevertheless, one must ask at what cost - the blade of public outrage is sharp and hard to control. At no point at no point in this process was their any room for fact finding or reasoned debate among the people aggrieved and affected by this.
We've let Stallman spam csail-related for many years to the point that it was a common joke for it to be called stallman-related in the lab ("Where'd you find your aparment?" "Oh, I posted on stallman-related - I half expected to get a moral lecture from him about the immorality of private ownership of real estate, but looks like he was busy"). Was it a mistake to let that happen so long on a list that everybody at CSAIL is automatically subscribed to, especially the new incoming students? Probably. Because of aforementioned rhetoric challenges his emails are not the best first impression of the lab community. I think banning Stallman from csail-related could have been a perfectly proportionate response here (as well as making him take down that stupid door tag). This all-or-nothing witch hunt, deeply concerns me.