There are a lot of gender expectations that punish assertive and matter of fact women as 'bitchy' and 'insensitive'. If a white guy behaves the same way no one thinks twice about it. To me it sounds like management at Github is uncomfortable with her perspectives. We often see women and minorities censured for not trying to conform to the model of a demure, inoffensive, and compliant minority.
Much like the comments here, Github management appears to prefer to focus on the perceived personality flaws of someone who makes others uncomfortable by her presence rather than underlying issues causing their discomfort.
The "insensitivity" mentioned in the piece appears to be largely based on the fact that the author behaves much like a white guy would in these situations.