As you said, people seem to fail to understand the nuances of something like this. It's entirely possible that he meant entirely well, but acted in a manner that was -- as they mentioned to his wife -- terribly naive, at least for a company of the scale of Github.
Just to give an example of such a nuance, in a tiny startup there might be occasions where everyone might have a big drinking and cavorting pool party at the founder's pad. As the company gets bigger, however, such activities become legal liability cesspools, and it would be very poor judgment because everything becomes a perilous he said/she said type situation. That is an extreme example, but it's why senior management often become increasingly insular and detached as the company grows: Because they legally have to. It sounds like Tom failed to do this.
Which is exactly what it sounds like happened here.
I kind of despise this blog entry because while it berates the unfairness of the old boy's club and so on, it seems to argue that any woman who claims anything should be treated as unequivocal truth, punishment meted out to the harshest extent possible. That is scary, but it is sadly where many of these conversations seem to go.
Not all women are honest and truthful. Women are not above pettiness, power plays and self-interests.