I think his words are being misrepresented.

He said this: " Minsky had sex with one of Epstein’s harem [...] Let’s presume that was true [...] We can imagine many scenarios, but the most plausible scenario is that she presented herself to him as entirely willing. Assuming she was being coerced by Epstein, he would have had every reason to tell her to conceal that from most of his associates. [...] "

I have no clue how plausible this scenario is, but I don't see any reason to infer anything about the character of Stallman based on him suggesting it.