The Doctor changes the past on Earth or in general all the time so he's also affecting his own timeline by changing past events that may shape future events he's involved in yet that doesn't stop him. He doesn't travel to his specific past and change events he was involved in "normally", as it could have cataclysmic affects, but traveling back to destroy a race in the ancient past isn't changing something specific in your own timeline. What I mean is for instance on the replica Titanic he could have went back and prevented the deaths that occurred, but that was an event he was actively part of. Theoretically he could alter the original Titanic as he wasn't on board...I guess lol, but he would probably argue that the Titanic is a fixed point in time. That being said I'd definitely label any ship capable of time travel as a super weapon, but that's my opinion.