In some eras, yes. It comes and goes. The Doctor is one of those heroes who never carries a weapon, though he does carry tools that can have secondary uses as weapons, and sometimes uses them.

William Hartnell's First Doctor doesn't strike me as pacifist at all, but it became more of a defining trait in the 1970s. Tom Baker's Fourth Doctor was very much the goofy, seemingly mad joker who disdained fighting, though his attitude toward it was more amused contempt than anything else. The Fifth Doctor paid a lot of lip service to pacifism, but always seemed to end up in bloody situations where he was effectively enabling violence or pushing Daleks out of windows. The new series Doctors aren't all that pacifistic but they have contempt for what they regard as needless or excessive violence.