Remember that Knuckles is a social caveman and has never closely interacted with a woman until Rouge shows up in Adventure 2 (Before Sega made it so Amy was his buddy in the classic universe, that is).
Realistically, he would get extremely hard just at the sensation of that hot voluptuous woman grabbing him by the neck. Then his natural primal instincts would kick in.
He doesn't have entire years of indoctrination to understand what he's doing. He is just following his urges like the recluse hermit he is. And oh boy does he rape her.
He throws that bitch to the ground, hops on top of her, and tears all her clothes off. That whore instantly regrets getting in the way of this unstable aboriginal. She cries and screams for help as Knuckles pumps her with lust he has never felt before, in a complete daze and consumed by his basic primal responses.
Eggman shows up with his gay-ass claw thing but is so instantly intimidated by this savage display that he just leaves.
After pumping Rouge full of his echidna seed and leaving her broken and mentally scarred, he throws her out of his island and gets back to his duty, curious about what had just occurred but ultimately unfazed. Simply satisfied with the experience and hoping to re-enact it again someday.

Fuck Rouge. Stupid bitch needs to get beaten and raped.