http://en.wikipedia.org/wiki/Alpha_%28ethology%29
The way her blog reads and the stories surrounding the GitHub incident indicates to me, she thought she was in charge and pushed people around, which turned a lot of people off. Alpha positions are earned, not given. When people come in and just expect to be the dominant personality, you get the issues she ran into at GitHub.
This doesn't take away from any of her allegations, but it probably was a role in the issues and friction she had with team members.
So when you say "In some of the environments I've worked in, women who have "alpha" traits are not looked upon favorably and detested by their male counterparts." you are saying that women who have traits that are pseudo alpha - in other words behaving as if you have the 'highest rank' when you haven't earned it or got it as a matter of fact, is the kind of behavior that men detest.
I guess my question is, unless there is something distinctively obnoxious about a woman behaving in this way, is this really a gender issue? There are plenty of men who behave like this aren't there? And my experience has been that both men and women don't like men doing it?
So it seems that either a woman doing it is doubly bad (which seems like a form of sexism - you can't even be obnoxious if you're a woman because it's distinctively obnoxious) or it isn't really a gender issue.
I'm not intending to pointlessly nit pick here. I am really interested in whether you feel there is something about a woman doing it that is likely, for whatever reason, to incite a more negative reaction. Could it, for example, be that men are very attuned to alpha dynamics and feel that they are being in some sense 'wronged' when a woman challenges them? etc etc?