Honestly, rape is allowed to be in yaoi and other works. But the difference between something okay and something not is how the serious topic is discussed.
This is honestly a bad example because it romanticizes rape as a fantastical thing that leads to love. Though it may be fiction, it doesn't treat rape as a serious topic. It's basically like how people add in a suicidal trope to characters without any depth and encourages angsty and negative tropes as an acceptable thing. (This is why we see so many edgy tumblr kids pretending to slit their wrists).
Rape and abuse are allowed in works of fiction when they shed light to the case and give the dark topic a visual on how serious it is. Many works like KS give us a psychological thinking of the predators and victims and help us understand the issue more.
Rape is a serious thing and should not be romanticized. Fiction or not it should honestly only be used as an educational purpose within a plot and not for a bunch of fujoshis/ fudanshi kinks.
Please support the author on WEBTOONS! It's totally free and in better quality!
http://www.webtoons.com/en/romance/days-of-hana/list?title_no=1246
So basically a kids menu. But instead of for children... it is the children.