Nathaniel blamed Minnie for allowing his children to grow so close to Aurora when she knew they needed to use the girl. If she had listened to him, Aurora would have been locked up somewhere until it became time for her to be of some use and his children wouldn't have to care about what happened to the girl.
He believed his mother was upset about something that happened in the past between her and the Aurora she knew and was trying to make it up to this new Aurora. The whole story about him having a mistress and a child outside of his marriage had been ridiculous in his eyes and the only reason he went along with the stupid plan was that his mother threatened him.
"Don't worry about Aurora and what everyone else is saying. Since Samuel can't confirm anything that happens, I will not hold it against you. And even though the two of you are not speaking, I like to think you wouldn't allow someone to almost kill your brother by knocking him out."