The accusation is that he made people uncomfortable, didn't do enough to change that when it was raised, and defended criminal behavior by insisting on distinctions that the authors of the report consider immaterial or harmful.
I worked for RMS/FSF briefly and I think there is something about his radical refusal to compromise on anything conceptual (to avoid conflict or misunderstanding, e.g.) that is fundamentally incompatible with running an organization. This is on display here.
So I think it's probably right for FSF and RMS to part ways, but I also think it's positive for the world for him to keep on insisting on moral clarity in his terms.
At the same time, everybody should read the whole report and decide whether they think RMS's insistence on the distinctions rejected by the authors is helpful or unhelpful. I think some of RMS's distinctions could be helpful to the cause of reducing the incidence of sexual abuse.