For anyone wondering who the guy was or what Tomoko meant, it's a callback to chapter 15 where she told Kii that he was her boyfriend. After seeing her with another girl Kii got upset and made a point to tell the guy off. Because she was lying she begged him for forgiveness, aka dogeza/"genuflect". It was also the first time Kii saw Tomoko as not her "perfect and popular nee-chan".
And yes, it was extremely painful to read.