Khan wouldn't exactly call the life Rodney had led as making up for what had happened on Nitis. After all, Rodney had mostly worked on restoring his reputation and serving humankind's best interests.
Still, Khan didn't disregard the challenges, either.
As a fellow struggler, Khan could imagine what Rodney had gone through to get where he was. Sure, their starting points had been different, and Khan didn't forget how Rodney's fall had happened because of his actions.
Rodney had lost what Khan never had due to his own mistakes, but that didn't make his rise to power any less praiseworthy. He had started later than Khan, and their paths and goals featured irreconcilable differences, but he had still done it to some extent.