I read some chapters of the manga myself. What she did to the MC isn't defensible, and she's absolute trash. I'm not asking you to feel sympathy for her, and it's fine to wish suffering on her I think.
That said, I don't think rape is appropriate as a punishment. I don't think torture should ever be condoned, but people are more touchy about rape in fiction than other crimes, because readers are much more likely to actually rape someone else than to otherwise torture them.
It doesn't matter much if readers think gruesome torture is appropriate, because it has little impact on how they would act in real life. Someone that thinks rape is an appropriate response to offense, may end up actually committing the act (drugging/getting someone intoxicated to have your way with their body is rape and happens uncomfortably frequently).
Many people are also acquainted with someone (usually female) that is a victim of rape.
It's not that people have double standards about fictional rape. It's that thinking rape is appropriate/justified can have harmful consequences in real life, so a lot of people oppose it.
All of the above said, I have enjoyed some rape scenes in the smut I read, and I have no intention of judging others' kinks. Enjoying a rape scene as pornography is very different from thinking rape is an appropriate punishment, and that's what I was objecting to.