
Did he rape him?

Yes Jinhyun raped Chiwoo. I heard the author herself confirmed it on her twitter. All of Chiwoo's actions were of a traumatized rape victim.
- Chiwoo’s bare legs, his pants were down. Their conversation in the recent chapter reinforces it ( http://www.mangago.zone/read-manga/back_to_school/uu/iur_chapter-41/pg-30/)
- Chiwoo says "how i kept pleading with you to stop". Jihyun did in fact rape Chiwoo as you can clearly see in this panel
( http://www.mangago.zone/read-manga/back_to_school/uu/iur_chapter-41/pg-31/)

Also here Chiwoo adjusts/puts on his pants again, with blood dripping from the back of his pants/legs (also ass) even though he didn't get glass shards in that area. Clearly that blood was from being raped.
( http://www.mangago.zone/read-manga/back_to_school/uu/iur_chapter-19/pg-2/)
I don't think any confusions left here.
Where's the new chapter?