'Evil' is only 'Live' backwards
No one considers themselves evil. This is the main ideal the Doctor takes into account when he travels. No matter how awful the actions of an individual or a species, they have motivations that are just as valid as any other living creature. These motivations are anything from simple survival, to money, power, desperation, or intolerance. They are all influenced by the species' needs and their culture; to them, their actions are the norm. For the most part, the Doctor respects this as long as other life forms are not being hurt.
Often times, he can recognise an injured party pretty fast, and does everything he can to understand the creature's motivations and come up with a compromise. The conversation is generally a brief exchange, just enough for him to understand the best course of action in the moment, but the question, "Why?" drives him to pursue the matter further. At times, he ignores cultural views in order to preserve a species, even at the expense of another species' discomfort (The Unquiet Dead). It is only when negotiations fail that he will take drastic action to save himself and others, even annihilating the threat if need be.
But what about the Doctor's culture? How much is it affecting his personal views and judgements? We only know what he has told us. It seems to be taboo to steal a TARDIS as he did, and likewise, to favour humans as much as he does. By Time Lord standards, he is probably seen as the slightly insane child who is blundering around with whatever human can put up with him.
His time with humans has both helped and hurt his concept of culture. On the one hand, it has made him more critical of his own species. On the other, he has likely gone from somewhat crazy to full out evil when he stood up to his people in the Time War. Because of him, the Time Lords lost and have all but gone extinct, with the Doctor as the only remaining survivor. To top it off, he sees this as a good thing. Is this not the definition of evil as we would use it today?
The Doctor is evil, but then, so is everyone else on the show, and the entirety of the human race. So maybe it's just time to stop using the word as if it has any meaning, and just agree that as long as someone isn't hurting anyone, they are not doing anything wrong. We can worry about the definition of 'hurting' and 'anyone' later.
