Good point; a complementary theory would be that women wish to obtain high status for themselves, and the perception that CS is low status turns them off. I don't see how we could distinguish between your theory and the 'Roissy theory', so it is equally valid.
As for intolerance, I'm not sure how we could consider your unwillingness to tolerate certain kinds of offices as anything other than intolerance.
Scratch off women and just say: "some people wish to obtain high status for themselves." Some people aren't as concerned with status - it's not that they don't care, but they're not willing to put up with as much crap to gain it. (Doctors and lawyers certainly put up with a lot of crap for their perceived status.) If we further assume there is an occupation with middle status, but has nontrivial social barriers to a certain group, then there's not much incentive for that group to break in when there are plenty of other occupations with the same status.
The differences between what I said and what you said: mine could apply to any group, not just women, and I'm assuming that only a smaller subset of most people are willing to pursue high social status despite the extra burdens; most people are fine with middle status.
Also, intolerance of an environment is different than intolerance of a group of people.
The article suggests that women are turned off by the perception of low status to a greater extent than men.
Regarding middle status jobs, there are plenty of formerly male-dominated middle status jobs which women have successfully broken into, e.g. advertising (c.f. Mad Men).
Any explanation of why women do not enter math/phys/CS must come up with something that distinguishes math/phys/CS from those other fields. Being a "middle status job" doesn't do it, nor does initial unfriendliness. I'd suggest that one possible explanation is that "geeky" pursuits are actually lower status than most comparable office jobs, and more women than men are turned off by low status.
Given the careers where women dominate (nursing, teaching, publishing, lawyering), I wouldn't believe any claims that women choose their careers based on their potenetial high status. Except maybe for lawyering. But I would bet that many more women lawyers are in social or environmental causes than not.
On the other hand, the idea of being repulsed by hanging out with low-status men… as a woman, that resonates with me.
The best thing that's happened for my happiness with programming is the arising of more well-rounded, socially skilled developers, who started off as music professors or linguists, like the ones I found when I switched to Ruby.
As for intolerance, I'm not sure how we could consider your unwillingness to tolerate certain kinds of offices as anything other than intolerance.