To be fair, the accusations have never been about persecuting on race and/or gender in such a strict sense - they're basically about the FSF deciding they didn't want the hassle of employing somebody who some other employees were harassing on the basis of gender identity.
Note that this doesn't require that the people who fired her are bigots so to speak - you can fully empathise with someone and still decide that it's easier/cheaper for the company to fire them than to deal with the problem, and without strong worker protections, that's possibly a perfectly rational thing to do. The FSF isn't particularly special in regards to the rights of minority groups and I'd expect it to behave the same as many organisations of a similar size. But the result is an organisation which tends heavily towards discrimination against people outside the cultural norm (who're more likely to be targeted and harassed, and so cost additional time/money/risk to employ), and that's something some people feel quite strongly should be fought against.