They did it because if Amicus lost emperorship, the MC would be taken away to somewhere safe. Also he was much rougher because he didn't care much about Neferu's feelings so it doesn't matter how Neferu feels. He cares alot for the MC so he wouldn't want to hurt him.
The reason why you like Amicus in the beginning is because you felt special and appreciated. This is more of a personal thing, but I see sex as extremely emotional. Meanwhile, it seems to be a common theme that the wolves see sex as purely instinctual. When you see Amicus with Neferu, if you were like me, yeah, you can forgive him (which I do) but I can't convince myself that it wasn't emotional because that would be going against my personal meaning of sex. It is clear that that's not Amicus's priority especially when he's trying to get a handy from you in the bedroom or a blow in the prison.
And honestly, being rough to me is a lot more passionate. If you're being rough with someone in bed I'd assume there would be a lot of trust, and the other person would probably turned on by the idea of you wanting them real bad. Although, I can completely understand if you see it in a different light :)