Summary:

1. Some economists (including Robin Hanson) said some things using rape as an example to illustrate abstract theoretical points, which pissed a lot of people off to whom rape is not an abstract matter. One of them (Steve Landsburg) also participated in sexual harassment of an activist. Some other economists (including Lawrence Summers) claimed that women are (relatively) bad at math and science.

Some yet other economists actually performed a study and found that economics has "a persistent sex gap in promotion that cannot be readily explained by productivity differences" and that "the average female economist -- unlike the average female physicist or mathematician -- is likely to have a better publication record than her male peers", and thus that economics as an institution is biased against women practitioners.

2. Robin Hanson vigorously agrees that economics as an institution is biased against women practitioners, but doesn't think his use of rape as a theoretical example has anything to do with that, and certainly that he didn't intend to minimize rape. Just the opposite: "Just as people who accuse others of being like Hitler do not usually intend to praise Hitler, people who compare other harms to rape usually intend to emphasize how big are those other harms, not how small is rape." He cites professional racist Steve Sailer in his defense, because that's really going to change anyone's minds.

3. Steve Sailer calls a bunch of people vile names. Yawn.

My conclusion: Robin Hanson is probably not personally responsible for the observed phenomenon of economics as an institution being biased against women practitioners. But the level of instrumental rationality and/or good rhetoric demonstrated here is not super great. If you want to convince people that you are not a bigot, why cite a bigot's defense of you as his ally?

Second, it isn't clear to me that the "badness" of using rape as a theoretical example has anything to do with minimizing it. Rather, it has to do with choosing to offhandedly mention something really awful which is linked to the victimization of a fraction of your students or readers. Being constantly squicked by gratuitous scary examples that selectively target you is not great for the concentration.

In a book about management that my partner S was reading recently, there was an analogy where managers are compared to ship captains. A page later, bad managers are described as "whipping" their underlings — that is, using punishment as an incentive. Now, S is from the West Indies, and the proximity of "ship captain" and "whipping" immediately reminded her of the slave trade, and gave her a pretty heavy-duty squick reaction. Does this mean the authors of the book intended to turn people off of being managers through stereotype threat or something? No. Does it mean they even intended to remind anyone of the slave trade? No. Does it mean that these analogies cumulatively had the effect of distracting S from the point the authors were trying to make? Yes.

If the authors were challenged on this, would they resort to citing professional racists in their defense? Probably not; they'd probably say something like "oops, wow, that was totally unintentional and really embarrassing."