https://www.mangago.zone/read-manga/kiraide_isasete/
Tbh this is the only one I can think of but it's also a bit angsty around the last chapters
it's hard to find any story like that :(
maybe https://www.mangago.zone/read-manga/beware_of_the_full_moon_in_march/ ?
both main characters at least understand and acknowledge that the bottom was raped by the top/ml
i think the one also fits the bill. the story doesn't go that deep about the bottom dealing with his rape though. by the end of it he *is* healing
https://www.mangago.zone/read-manga/back_to_school/
As in, its not just used for 'hot sex' but its the traumatic experience that rape and abuse usually are. i think ive only ever seen one uke that actually got ptsd from his attack. are there any yaois that take this seriously?