I don't think this argument makes sense. In fact if we follow it to its conclusion, it's an additional reason for RMS to be removed from his job.
1. RMS is not being punished by the FSF.
He does not have any right to a particular job, even as the founder of an organization. Many people, including FSF board members, believed he was not competent to serve the organization in a leadership role.
One could argue about whether getting excoriated on social media is a "non-judicial punishment". Perens seems to be decrying a rush to judgment, contrasting it with jury duty. But the most damning criticism is coming from people who worked with RMS closely, and who for years even shielded him from the consequences of his own actions. These people have thought long and hard about their experiences.
2. RMS is not obviously asking for any understanding nor promising to be better.
RMS has publicly described himself as having autistic characteristics. He seems to be saying he's sub-clinical. But, if he believes that this is the source of his difficulties, this is a private matter between him and his employer. So, our ability to judge here is limited.
However, at least from public statements, he does not seem to be invoking that defense, or asking for understanding. In fact, he doesn't seem to be even interested in any harms he has caused. Surely this would be step one?
Perens may well believe that RMS' problem is autism. But it matters what RMS believes and does. If he really has a disability but is denying it has any impact, this is even more of a reason to remove him.
3. Frankly this entire argument does such a disservice to the many men and women who live with autism/Asperger's Syndrome. A lot of them do struggle with norms. But they also feel bad when they inadvertently cause others pain. And most of them find a modus vivendi with others. This seems very unlike how RMS' interactions have been described, including to me by people who've worked with him, and what I've also personally seen at public events.
4. Personally it makes me very sad that we're having this argument. I don't take any pleasure in seeing RMS removed from a position of honor. I think he's one of the greatest thinkers of his time, and documents like "The Right to Read" ought to be in textbooks. There ought to be a place for RMS in our discourse. Just not this one.