The Doctor isn't a pacifist.
AN: My verson why he hates guns and being called sir. Please enjoy and review!

They think the Doctor is a pacifist.
Just because he dislikes guns and being called "sir" and people dying.
And to be fair to his myriad companions when he is asked he usually rambles on about guns being only made to kill (and that's a lie because they can be used to distract, to bluff, to incapacitate, to threaten and if he's lost his sonic to open doors in a rather permanent manner).
But it isn't the truth.

The real reason he dislikes guns is that they are so basic. Time-lords manipul- used to manipulate radiation when they were still in the nursery while humans are forced to use nitroguanidine powder in their guns. The majority of Gallifrians could manipulate time itself (simply siphoning off years of time from the environment) to simply erase people from existence (which was so much easier to clean afterwards). He would use them if he had to despite the crudity of the things (but he would always check it surreptitiously before using it because he had seen how guns- any gun – could be misfire or be made to). He doesn't trust them.

But he hates being called "sir" (like he hates Daleks and the cruelty humans can do – to each other and other innocent worlds – and occasionally himself).

There is a limit to the different syllables any Timelord (or human for that matter) can make.
Gallifreyan – especially the Old High Gallifreyan – is a musical language that flows off the fluent speakers tongue.
The curter sharper syllables were used in the insults, expressions of dislike of hatred...
and most specifiably the word traitor.
Not in the usual betrayer of trust though that stung enough but in the declaration that this being (not even a person any longer) is a killer of family-traitor to the council-murderer of many that they shall never be know by their chosen-name-but by their deserved title-betrayer-scum of Gallifrey-thechildthatneverwastheirs.

Because if the Gallifreyans, the Time-lords were able to speak to him that's what they would call him.
And the humans speak it as a sign of respect in their ignorance.

He dislikes watching humans die. (And some small part of his brain says it's is only because they look like Time-Lords that he cares at all, but he knows -hopes- that isn't true -but it was once, wasn't it?)
Even if they are the "bad guys" (because if they are bad – what exactly is he?).

He cultivates these dislikes (these handicaps) because they keep them safe, they limit him, encourage him to be inventive to find a way so no-one dies.
But occasionally he fails and shows a small amount of his power, of his abilities, his talent at utter destruction.
And sometimes his companions see it and are reminded that the Doctor - although he is many things – is not human.

He isn't human at all.