There are speech rights that are not protected legally, rather based on culture, tradition, and so on. I don’t know what these are like at MIT, but they are fairly broad in a lot of western educational institutions.
Those aren't "rights", those are "norms." When you engage in exceptional behavior (like suggesting a child sex slave's docile appearance excuses Minksy'd responsibility to not rape kids) then your norms may find themselves superceded.
But ultimately RMS's positon was one of political, not technical, leadership. With no more supporters, the FSF rejected him. Without the FSF, what purpose could he serve at his job?