Hmm... I think the series likes to think it is ambivalent about the Doctor but I feel that ambivalence is a long way down its agenda so much so that it easily falls into the trap of appearing to peddle an "all aliens are evil" line which get people like Lawrence Miles so hot under the collar. The Doctor occasionally does questionable things and, even more rarely, someone says to him "that was a bit questionable", but the closest they've come to actually showing this (the idea that Saxon rose to power because of the void created by the departure of Harriet Jones) they backed out because accessibility comes higher up their agenda.

The end of series 1 they have the Doctor effectively say "I created all this" but in that situation his actions in the Long Game were considerably less questionable than many since. I think its very hard to truly question the Doctor's actions without being prepared to show consequences a bit more thoroughly and both Doctor Who and, I think Torchwood, suffer from an anxiety that showing ramifications from story to story will lose the casual viewer.