You and Jim raise very good points but I see the reason elsewhere. The act of rape is political in a sense that murder rarely is: a rapist disrespects the very fabric of our communal life (not just a maybe honorable man), a system heavily relying on honor by means of the exchange of "pristine" women; he not only devalues a commodity (her chastity) in maybe great demand, he gravely diminishes the overall pool everyone draws from; there's now almost nothing to be gained from having her/giving her. The intense actual mental and physical damage done to the victim is of comparatively little concern to people fervently asking for a rapist to be tortured, then lynched.
Things are much more subtle and/or sophisticated these days, but that line of thinking is still very present. People will much rather tolerate disrespect towards the male members of their family than towards the female members (just think of the popularity and effectiveness of mom jokes), but not because they think more highly of the latter, quite the opposite. If you call somebody's mother (or sister) a "whore", to take a drastic example, you raise the honor of the entire family (or its capital in the case of an unmarried sister) to question; the males and their honor are represented by their women (whom we narrowly watch showing chastity, raising the children, adorning the house and their husbands, covering their backs, caring for guests, easing discord, appealing for charity etc.). It might be another reason why promiscuous men are accepted while promiscuous women rarely are; if a woman is (seemingly) available to all, she can't be given/owned. And here the rapist figures in: he, too, treats women as available to all.
That's what we can't tolerate, the harm to our way of thinking, not that to the victim, that's mainly a rationalization. We aren't necessarily showing great insight into the complexities of ethics if rape seems worse to us than murder. We hardly differentiate between a rape victim and a women in control of her sexuality; they're valuable things. It's quite disturbing.