For one, that Facebook post read pretty much as described above. Comparing someone who complains about vicious, nasty humor like "rape-me" and "recursive_pimp_slap" in a highly public place to "women who want to make it all about their vagina" and saying that people are "co-opting male spaces" pretty much says exactly that. It says "yes, it's hostile to women, and any women who complain can be reduced to a single anatomical feature, and if you complain you're trying to co-opt my playspace." There's really not much wiggle room in interpreting it.

a certain faction of extremists

The problem is that many people who are making reasonable points, like someone who's pointing out that gems named "rape-me" really aren't acceptable in polite society, wind up being lumped in with extremists.

There may be a few extremists out there, but not many. What you see lots more are people who are tone deaf and make problems worse by going around and yelling "you're racist/sexist/homophobic", "no, you're a feminazi/PC", and on and on without ever really getting anywhere. Most of those people (on either side) aren't extremists, they're just caught in the internet spiral of hate. But just because some people go overboard on the internet spiral of hate that simply amplifies problems, doesn't mean that there aren't some real problems.

So, responding to someone who says "rape-me is not an acceptable name for a gem" with such rhetoric is instantly escalating that internet spiral of hate for no reason. Lumping people who have legitimate complaints, like "let's not have rape references in our public software repositories" or "let's try not to sexually assault people at conferences" with "extremists" is a way of dismissing those legitimate concerns and simultaneously escalating the rhetoric to the point where nothing useful will come of it.

whinging about a Torvalds rant on the kernel lists,
or the extended brouhaha from the "donglegate" thing
from earlier in the year

These are two very different issues. One is a question of whether it's a good idea to chastise your collaborators so strongly on a public list, or whether there could be more polite ways to make your opinions known. It didn't really have any kind of discriminatory or sexist content, simply a question of the best way to encourage good practices and discourage bad ones.

The other is somewhat more relevant. It's an example of puerile humor, in a private conversation that happened to be in a public place (at least, as far as I've been able to gather). I found that it seemed to be an excessive attempt to shame people for behavior that was, as far as I can tell, supposed to be private, but was in a public place so other people could overhear it. I think that there is some reasonable debate to be had over what kind of behavior is appropriate in a public space where you can be overheard, but that there was an overreaction to it, since it was private behavior. However, the internet spiral of hate wound up blowing the whole thing out of control, in part because there are so many people who are so sensitive on both sides of these issues, and it went way beyond anything it should have.

Here's the thing. Donglegate could have been someone pointing out behavior that she considered inappropriate, and people could have taken that to heart and moved on. But lots of people overreacted. Posting people's pictures online publicly, rather than either talking to them yourself or letting PyCon staff talk to them, was an overreaction. Firing one of the people involved in the conversation was an overreaction. Firing Adria Richards was probably an overreaction, though at that point she had shown herself to be divisive enough to not be very good at community building. Sending her death threats and calling her a slut was definitely an overreaction.

So you can see several areas here were there were massive overreactions that led to this being far larger than it should have been.

Likewise with this post, the original post was a fairly reasonable request. "Let's not have nasty, rude things like rape-me in highly public, visible, and widely used code repositories". Now, some of it may have been a slight overreaction, like mentioning "hoe" (which is a clear reference to "rake") along with these other items. But what's a good way to deal with that? Probably to discuss those specifics; say that "rape-me" and "recursive_pimp_slap" are pretty clearly inappropriate, but there's really no problem with "hoe" or "therapist", and maybe discuss his point about whether there should be an explicit filter versus applying a certain amount of judgement. Those are reasonable, appropriate ways to respond to the post, that won't lead to donglegate style escalation.

Talking about "vaginas" and "co-opting of male spaces" is, well, the opposite.

At what point is it socially acceptable to express
exasperation with a group of people who ostensibly have
noble goals, but then cause damage while they're at it?

It's generally socially acceptable to express exasperation with a group by pointing out specific flaws in their arguments, offering constructive criticism, and trying to de-escalate the situation. You should also be aware when doing so of whether you might be blind to some real problem, and that your response could come off as dismissive of that real problem; so you should try to first identify the problem that is being addressed, and understand why people consider it to be a problem.

At what point is "this is not a 'safe' space, (not in
that people are going to go out of their way to offend
you, but in that people have better things to spend their
time on than measuring their every word for the slightest
hint of '$ism'), so you may hear things that offend you,
and how you choose to interpret and deal with that is
entirely on you" ...an acceptable response?

Hmm. When people refer to a "safe space", they generally don't mean that no one is ever going to be offended by what someone else says. No one is going to measure out every word that they say, and always avoid stepping on someone's toes.

A safe space is instead one where you feel comfortable telling someone when you think they crossed the line, that they will respect that and not attack you for it.

One thing to keep in mind is that what's appropriate in one context may not be in another. Among close friends, you may feel perfectly comfortable telling racy jokes, or jokes about Jews or Catholics or blondes or what have you. When you're in the office, or at a conference, and there are people you don't know, you should consider that they may not take those jokes the same way that your friends do.

Think to yourself. If you have to tell someone "this is not a safe space", you are basically telling them "I do not want you in this space." Because if you want them in that space, you will make it safe for them. You don't have to tell your friends that, and can crack all the offensive jokes you want with them, because you know that they will be OK with it. But if there's someone there you know will not be OK with it, and you crack the joke, then you are saying to them "I would like to hurt you." Now, there are obviously nuances; sometimes you may crack the joke and only afterwards realize that it went to far, at which point you could choose to apologize and diffuse the situation (or make another making fun of yourself, depending on the circumstances).

On the public internet, recall that you can never be sure of who will see your joke, and how they'll react to your humor. Things you post to the public internet should be things that you are OK with your wife seeing, your grandparents seeing, your kids seeing, your buddy back from Iraq with PTSD seeing, a battered wife seeing, a child victim of sexual assault seeing, and so on.

If you want to do off-color jokes publicly like that, be sure to have a thick skin, because someone's sure to be offended and start trying to escalate that internet spiral of hate. This is where Penny Arcade slipped up; I think that the original Dickwolves comic was not a bad comic and not particularly offensive; in fact, it was lampooning ambivalence towards horrible things happening inspired by game design. But of course there was someone out there who got offended, and they made the mistake of taking offense at the offense and continuing to escalate the internet spiral of hate.

Sometimes, you do need to think to yourself and say "yes, I am OK with offending you." There are some people out there who try to pick apart everything and find something to get offended about in it. If you publish something publicly, you can't ever please them. But if you do, stop for a minute and decide if you really do want to offend them, of if maybe you'd rather let them be. And if you are sure that you are OK with offending them, then be sure of it, say your piece, and be done with it. Don't try to tell them why they shouldn't be offended. Don't make fun of them for getting offended. Just leave it be and move on.

(Note: same answer has to apply to pretty much any
'$minority rights' group behaving badly)

I'm curious why you call out minority rights groups. There are lots of different organizations that may have goals you agree with, and techniques you disagree with, or that you find damaging. Why do you specifically call out minority rights groups for "behaving badly"?