i don't know which animes you're talking about, but here's my two bits:

Rape is worse than murder (in media), because we have a living victim.
And actually, I think that having a villain cut off / torture a person and letting that person live would make him less sympathetic than a villain that killed a person and chopped off the entire body. So mutilation is also worse than murder.
I'm also willing to go and say that necrophilia is probably more sympathetic than rape.
corpses (and murder victims in media) are things, objects. as audiences, we don't have any identification with them, so a character can kill millions in a show, but when we judge whether we like him or not, he is the only contestent, so we identify with.
If there's a living victim, then we have two sides, and we judge the evil character much more harshly, becuase the actions are weighted against their effect on a living character.