Well you can kill Burke who's just sitting on a chair or numerous others with Evil Karma and you gain karma for shooting them in public and it's considered a good thing. Colonel Autumn is another one of those "special" characters besides the Overseer who you can spare and consider the importance of human life after plowing through dozens, possibly hundreds to get to them.
So many characters in the narrative are completely and utterly disposable, like the guards, or old woman who dies in the cafeteria, or the couple who both get shot trying to escape the Atrium and never mentioned again. But with some characters, often leaders of the groups who initiate the whole thing, are the only people that count as real characters in the narrative. I'd already shot 6 or 7 people, killing one more isn't going to desensitize my Lone Wanderer anymore.
Don't get me wrong, I know why they do it. Any game which is combat focused has this disconnect between the narrative told through the story and the narrative told through the actual game play. If the primary game mechanic is killing, then you have to have things to kill and fight.