Hoo boy... The light of the next season gives way to discussions of Doctor morality.
The Doctor has been his own conscience, answerable only to himself, since the dawning days of William Hartnell, especially against the first alien OF the series (You guessed it.), the Daleks. There has never been a time where the Doctor has not attempted to greatly-eliminate the imminent threat, even in totality. Daleks? Always. And the first iteration of the Cybermen featured...the destruction of an entire fleet of Cybermen and the planet Mondas. If it has no capacity for mercy, the Doctor finds it an acceptable target, as does anybody else who likes living.
There ius some question as to how he treats the Sontarons and Rutans, who are STILL fighting each other in their war. I would wager that he juxtaposed them into killing each other for the sake of the rest of the galaxy, never letting either side get a foothold. The funny part is that he may be trying to teach them the futility of war and unfortunately failing. We don't know.
The basic idea of the Doctor is that if you seek only malevolence and carnage in the galaxy, he has very little time for you, a point which has been very obvious since Sylvester McCoy, planting Xanatos Gambits to deal with many of his enemies. And it HAS been leading somewhere. You know it has. There is a point, even if continuity in the show is a full-blown cluster-flux. It is worried, it is alluded to plot-wise, that of all the things which may or may not be fully canonized and not timey-wimey'd inside-out, the results of The Trial of the Timelord may yet come to pass. Ever since THAT episode, the Doctor has been somberly aware that he is his own worst enemy...
