Punishments should have limits, but the point of removing a toxic member of a team is not to punish the individual. If I hang out with a group of friends, and one of those friends repeatedly makes some of the rest of us uncomfortable, I will stop inviting that person to our gatherings. This is not meant as a rehabilitory or a punitive measure. It's simply a group of people who aren't comfortable with someone else's presence asking that person to leave.
Stallman was removed because many found his presence unacceptable to their continued participation. Having removed him, that remains the case.
In addition to being poorly reasoned, this article is also somewhat contradictory. First, it argues that shunning should be temporary because the shunned must be given a chance to prove that they have reformed their behavior. Then it argues that Mr. Stallman's behavior is clearly based in his handicap and accommodations must be made for it. These two arguments don't work together. If he can control his behavior, his handicap need not be accommodated. If he cannot, there is no point to reassessing whether he has reformed.