No matter how many thousands of people he saves, or how much he's revered by those around him, there's no getting away from the fact that the Doctor is a seriously flawed individual.
From putting his companions in consistent peril (which often results in them dying, being left behind, or becoming scarred in some other significant way), to that time he, y'know, destroyed his own people during the Time War, he's caused plenty of messed up situations in his many years of existence, not least of which are all the times he's killed - unintentionally or otherwise - those who oppose him.
To give him some credit, he does try and avoid the loss of life where possible, but given the inherent dangers of parading throughout the universe and interfering with various life forms, peace isn't always an option - often, the main side effects of his adventures are collateral damage, injury, and death.
And on that point, the Time Lord has directly taken a life on more than one occasion, whether to save his own skin, protect a companion, or just to prove a point.
8. He Shot A General While Trying To Save Clara
Hell Bent finds the Doctor in full-on "I don't give a crap" mode. After spending billions of years trapped inside his own confession dial, it was clear that he'd go to any lengths necessary to undo Clara's death, which had happened a couple of episodes ago.
To do this, he uses a Gallifreyan extraction chamber to pluck her from her time stream literal milliseconds before her demise, which allows him to see her and talk to her once again. The only problem here is that her death is a fixed point: eventually, she'll have to be returned to her proper place so she can die, since her death is a concrete event that cannot be altered.
But ever the rule-breaker, the Doctor doesn't care about any of those details. Instead, he grabs a gun and holds a Time Lord General (who had just helped him retrieve Clara) at gunpoint. The General doesn't want Clara to leave out of fear that her existence will cause fractures in time, so the Doctor - completely blinded by his desire to let her live - pulls the trigger, shooting him in the chest at point-blank range.
Now, the reason that this entry is at the bottom of our list is that the General can and does regenerate: in this case, he changes from male to female. But still, it's been said that regeneration feels like dying, and the Doctor's murderous intent was clearly there.