https://www.mangago.zone/read-manga/deadlock/
This has the best depiction of rape trauma imo. And the mc isn't a weak person either. He's a tough detective who can fight well but when he gets raped (it's a spoiler I'm sorry...) u can tell it really affected him. The ML isn't involved in it but he helps the mc overcome the ptsd
back to school
Contains spoiler :
I don't really remember the plot but I do remember the bottom had to take a long time to move on from the sa. And when the perpetrator tried to get back with him, he was rejected since bottom has moved on and already got new bf.
Info : there is a side story of what would happen to bottom and perpetrator if the sa never happened.
OUROBOROS
https://www.mangago.zone/read-manga/ouroboros_1/
Boy meets Maria
https://www.mangago.zone/read-manga/boy_meets_maria/
Back to School
https://www.mangago.zone/read-manga/back_to_school/
You're welcome ~
I'll suggest another one then (if you haven't read it already), i just remembered it addressed rape as a very serious matter too, with no romanticizing and turning the page like it was nothing:
A Painter Behind the Curtain
https://www.mangago.zone/read-manga/a_proxy_painter/
Where the MC is actually traumatised by being SA'd/raped etc and it's not treated like nothing the day after? And preferably where the ML is not the assailant/rapist.