Increasing the rationality of a population can lead to that population being worse off, even by the "rationality as systematized winning" definition, if the members are at odds with each other. You don't necessarily want your adversaries to be more rational. But the reason that part made me cringe is that it carries so many caveats that it's incredibly misleading. There are many contexts where defecting in a prisoner's dilemma is a predictably bad idea, and rationality already has image problems as being rigid and unadaptable as well as antisocial without reinforcing them.
The video probably couldn't really have gone into a proper discussion of what variations of the prisoner's dilemma make defection appropriate without breaking the flow, but it really wasn't helped by a message of "paradoxically, rationality can leave you worse off."
I agree with your point that usage of rationality this way exacerbates the problem of straw-vulcanism. I'm not sure the criticism is aimed at the lowest hanging fruit in this case, but your point is well taken.
Your point about the dangerousness of rationality is not on point. I am almost strictly better off in a society in which the members are not at odds than in one where they are at odds. But whether one of the exceptions to that statement applies does not appear to depends on how dangerous individual members are. Unless individuals are so dangerous...
It's a brilliant idea: a lecture by a cool modern thinker, illustrated by word-by-word doodles on a whiteboard. Excellent at pulling you along the train of thought and absolutely disallowing boredom.
The lectures' content is pretty great too, although there's a definite left-wing, populist bent that's exploting today's post-crisis hot button issues (they got Zizek, for god's sake) - some might not like it. Regardless, it's all very amusing and enlightening. Been linked to before in a comment or to, but it deserves a headline.
You can start here: http://www.youtube.com/watch?v=dFs9WO2B8uI&feature=relmfu (But they're all worth watching!)