"You are a good Dalek." This phrase and the original ("You would make a good Dalek.") make more sense in this episode. The first one described the Ninth Doctor who, at the time, was angry at the Daleks, the Time Lords, and himself for the Time War and losing Gallifrey. He tried to destroy all of them only for it to be in vain. All that rage and hatred he felt because of it was being channelled towards that lone Dalek in the titular episode, who remarked on it because only the Daleks could have felt more anger and rage at that point. In this episode, however, "Rusty" remarks that, while he is not good because he still only feels hatred, the Doctor has seen both the good and bad of the universe and chooses to be good.
It could also be that, looking into his mind, he saw how the Doctor sometimes felt the Time Lords could be just as bad and destructive as the Daleks. Him being a good Dalek would be the same as calling him "a good Time Lord", but the latter statement would probably just enrage him.
The Doctor's insistence that Daleks can be nothing but pure evil has already been proven untrue in front of his own eyes in the forms of Daleks Sec and Caan. However, there are legitimate reasons why the Doctor wouldn't consider them as proof Daleks can be good. To start, as members of the Cult of Skaro, they were given independent thought and agency in contrast to the average Dalek Rusty started out as. And even then, Sec and Caan's Heel Face Turns were triggered by unique circumstances; Sec because he turned himself into a Dalek-human hybrid, thereby assimilating humanity's good traits into himself, and Caan because he broke through the Time War's time lock and thus saw all of time all at once, exposing his already independent mind to his kind's evil. Thus, one would forgive the Doctor for thinking that a Dalek's chances of turning good requires such specific and improbable circumstances that it might as well be zero.
