The villain committing an act of rape is treated as evil and morally reprehensible, but no more or less so than the numerous acts of murder and torture they had previously engaged in.
Rape is considered to be morally reprehensible, but less so than murder; perhaps a reasonable position given that some rape victims are eventually able to recover and return to normal lives, but a murder victim will never recover from being dead.
The writer feels that this trope is a bit overdone, and seeks to subvert it by having a character commit a rape and then be portrayed as sympathetic later. However, his editor believes that this will cause a backlash from readers and Moral Guardians everywhere, and thus "strongly encourages" the writer to change the story so that the rapist dies a painful death.
The author or a friend/family member of his/hers is a rape victim
Two random mooks are preparing to violently rape a woman in an alley. One looks at the other and says "Isn't it weird how, even though the psychopath we're working for is going to blow up the earth, we're still seen as more monstrous because of stuff like this?" His friend agrees, just in time for the hero to swoop in and violently execute them.
Discussed: "Hmmm... I'm bored with kicking puppies. How about we go the next level and rape?"
Conversed: "Wow... That kind of evil is above and beyond!"
Deconstructed: Because rape is considered worse than anything else, only rape is eventually considered a crime in the setting. Which means that killing people, Cold-Blooded Torture, genocide, killing children, starving people to death etc. is considered perfectly acceptable as long as there's no rape involved.
Reconstructed: People become more reasonable and, even though rape is still a revolting crime, it's not placed higher on the evilness scale than crimes that are just as bad or worse.