It came up in "Death in Heaven." Clara called out the Doctor on letting bad guys, especially Missy, escape to cause more death and destruction, and told him she'd hold him responsible for everyone Missy would kill in the future if he forced Clara to let her go. And the Doctor refused to let Clara do it and (was about to) do it himself so she wouldn't have to live with killing her.
This season has been lacking in nuance and thoughtfulness regarding the Doctor's pacifism. Graham and her could've had a very similar conversation with only a couple extra lines ("Doctor, we let that monster get away, and he killed that woman, and all the people on all these other ships. If we let him go again, we're responsible for all the hurt he'll cause." "Graham, we didn't stop him for good. That was my mistake, and my responsibility, and I'm going to fix it my way. More killing is not the answer." "Fine, you can stop him your way, but if I get to him first, I'm stopping him with mine.") that actually touched on the fact that the Doctor didn't merely allow, but in a very real sense facilitated uncountable atrocities.
There was a similar part in "Arachnids in the UK" where the Doctor specifically observed the giant spiders were too big to survive, and their lives were constant agony, and the best she could come up was to wall them up with a cache of food so they could slowly asphyxiate over weeks or months, and she was horrified that Mr. Big decided to kill the spider quickly, when her solution was also to euthanize it in the slowest possible way. It didn't make sense, except in a weird, "keeping your won hands clean is good enough" way.