Well, no I think he didn't kill the rapist because the uke was there, he probably didn't want to scare him by tearing another person limb from limb infront of him, but I have the feeling he'll hunt down the rapist later.
Totally, he killed a person who just cared for the uke, two of them. He will NEVER let anyone escape cause the seme is possessive a fuck(〜￣△￣)〜
If I remember correctly from the main story the seme didn't kill the sempai. The infirmary doctor killed him. If I remember right the senpai was bullying the other kid who is dating the doctor.
He killed someone who was kind to him (the uke) but he let the RAPIST live... Aghhh (╬￣皿￣)凸 This manga would be fine if the rape didn't exist or at least he had arrived to save him earlier... ┗( T﹏T )┛