Looking through some of the issues on that repo, the amount of bad faith people have in the very idea of a code of conduct is astonishing. Not to mention the sheer ignorance of issues affecting minorities within the tech community (seriously, Jon Stewart could have had a weeks worth of material). Sure, the wording of the code of conduct wasn't perfect, but it'd be much nicer if people wanted to see it improved in goo…
If you try to think about it in a clean-slate way, sort of; forget "oppression", "microagressions against minorities" and all the other politicized jargon that the current version is peppered with, and ask yourself (answers are my opinions, obviously)...
Q. Is there a problem with some open source communities being too hostile, unwelcoming, potentially harassing to many people? A. Yes. Some communities are clearly much more "nice" than others. Some are clearly much more welcoming of newbies, etc.
Q. How does this "bad behavior" manifest itself, in actual open source communities? A. Mostly by how much rudeness and brusqueness some regulars of the community feel they can treat others with. If you hang around on forums, issues, IRC channels etc. enough you can get a clear feel of the "niceness meter". Sometimes there's also explicit misogyny, but that's relatively rare. Other explicit forms of hostility (e.g. racism, transmisogynism) are even rarer to nonexistent. It's simply that if the overall level of niceness is low, then people behave like assholes. Asshole-like behavior is easy to interpret as racism etc.
Q. Is this a huge problem? Should we invest effort in trying to make communities more nice? A. I don't know, seems like a personal call. I personally like the nice and welcoming communities much more, and don't really see the point of being rude and hostile (I think it's counterproductive and not only wrong).
Q. Is a code of conduct a way to achieve that? A. Doubt it. Seems like the norm set by the leaders of the community, together with a few clear examples of "we will not tolerate this kind of behavior", is how it's successfully done. Is there a project which went "not nice -> adopted CoC -> became clearly nicer"? I haven't seen any.