The Doctor isn’t sure whether the term ‘pacifist’ fits him or not. On the one hand he abhors violence and the use of weapons, preferring to find peaceful, non-violent solutions to any situation he and his companions might find themselves in. Killing disgusts him, and taking lives denies those killed a chance to redeem themselves.
On the other hand, if fighting and even killing becomes necessary, as in his endless war against the Daleks, he can and will destroy his enemies wholesale.
He tries to keep his dark side buried, hidden from sight, but he’s always aware of its presence.