
It's meant to mock the advent of their developing relationship by incorporating elements of carnal lust and defilement, twisting the blooming subtly of simple, mutual coexistence into a blurred mess of the violent, uninhibited sex lives they both have been "groomed" to live under.
Judeo-Christian sentiments of Westernization have put sex culture at odds with concepts of purity, kinship, and clarity.
Essentially, Karino and Kuze wanted to assert dominance by implying that there is no avenue through which either Azusa or Atsumu can attain reprieval from the encroaching loss of control and hope that comes with becoming a "submissive." Using BDSM terminology here, because it really does appear fitting this time around.

Aw man your explanation's so complicated and technical, couldn't understand anything, but my English isn't very good I guess lol

...so why didn't he tell the teacher in the end? he had the chance.

I think it was mostly punishment for Atsumu for wanting to tell the teacher, but also for Azusa when he threatened to out Karino in chapter 4. Remember how Kuze said "that guy" can't keep his mouth shut?
I think breaking the friendship was secondary. The semes mostly want to protect the game and their power base. The rapes were also meant to humiliate and degrade them so they would never meet each other's eyes again. It's all about power and control.

It's just had a lot of vocabulary, and the sentences have a slightly more complex style. Suffice it to say that the Western world find sex culture corrupt and "anti-pure." Making them have sex was meant to mock the purity that Atsumu and Azusa experienced in becoming friends, and the act was also meant to rob the boys of their sense of control.
But whats the point in having them fuck eachother? Kinda lost me at that one... Is that supposed to be punishment?