OK but all those clips were old Dr Who.. This seems a thing only in New Who hence why I made the topic. But it's always open to interpretation..
I was too busy with work to list out all of 9-12's kills. I can do that now though.
Ninth:
Used a vial to destroy Nestene.
Rose
Allowed Lady Cassandra to die due to heat of Satellite 5.
The End of the World
Gave Mickey the codes to U.N.I.T. and told him to fire a missile at Thames House, in order to destroy the Slitheen family.
Aliens of London/World War III
While he didn't kill the Dalek, in
Dalek. He did build a gun to destroy it, before the Dalek killed itself.
Same goes with
Bad Wolf/The Parting of the Ways. When the Doctor built Delta Wave to kill all the Daleks, but it would also destroy the human race.
Tenth
The first casualties of 10, would be during the
Rise of the Cybermen/Age of Steel. All those Cybermen 10 destroyed through various means.
Ten killed the Racnoss and all her children in
The Runaway Bride.
While Ten did not kill the Family of Blood, in
Human Nature/The Family of Blood. His methods of imprisoning them and by extension making them immortal was disturbingly cruel.
Finally you have Meta-Crisis 10 killing all the Daleks in
Stolen Earth/Journey's End.
Eleven
If you consider the Weeping Angels living beings, the Doctor had them all sucked into one of the cracks in the universe.
Time of the Angels/Flesh and Stone
After Amy gets kidnapped, the Doctor scours the Universe looking for her, and blows up a Cyber Legion, while looking for information.
A Good Man Goes to War
11 leaves Solomon to his fate in
Dinosaur's on a Spaceship.
Finally, 11 combats and fights scores of his enemies on the planet of Christmas for centuries in
The Time of The Doctor. The big finale being 11 blowing up a huge Dalek Fleet.
Twelve
Kills that cyborg thing in
Deep Breath.
Kills the Sheriff in
Robot of Sherwood.
It would take me considerably more time, to outline all the people the Doctor either "manipulated" or inspired to do something violent. When I think of the Doctor being a manipulator, the one that comes to my mind is 7.