Yeah, Irving is without a doubt worse than Waiters defensively, but he makes up for it by being one of the best offensive PGs in the league. Waiters isn't really making up for it right now. His scoring comes and goes, and when he isn't scoring, he's been hurting the team. Doesn't rebound, doesn't pick up assists, doesn't play defense.
He'll turn it around at some point though, but for now, you can't blame Scott for benching Waiters when he isn't bringing much to the team and isn't really even making an effort defensively.