Who decides which are the questions that a representative of the university can ask and which will lead to punishment?

As far as I can tell, the discussion was on-topic given that a former professor, Minsky, was being accused of "assault." Stallman's questions and statements revolved around the use of that term and the trouble that its lack of specificity brings.

The university is (ideally) full of scholars holding controversial views, asking uncomfortable questions, and being accused of all manner of crimes. If one of them (Minsky) can be tarred and feathered without a trial, any of them could be.

I don't know what kind of world you want to live in, but I enjoyed my university experience where most of my professors were scholars holding more or less banal views and, to the best of my knowledge, not a one being accused of "all manner of crimes." I don't think professors being accused of crimes is either common or beneficial to the spirit of learning and scientific inquiry.

>but I enjoyed my university experience where most of my professors were scholars holding more or less banal views

If their views are banal, then there is likely nothing novel academically coming out of them. That’s literally the opposite point of professorship, tenure, and academic inquiry.

I recommend you look up the definition of “banal” because you either used it wrong or you don’t know what the point of tenure is.

Technically we don't know for sure what the punishment was for. Especially given that he's said much worse things in the past without resigning, it's possible that these resignations were forced because of some yet worse comments which haven't become public. And even if all of the relevant material is public, it seems likely that this is just the culmination of many issues and the FSF board and supporters simply ran out of patience for rms's antics at last, and that the tone-deaf and bizarre defense of Minsky was just the last straw.

https://gfycat.com/negligiblesmugfirefly