I think the problem with it can best be described using the trope "what measure is a mook?". Abbey and the pregnant lady, oh you should feel bad about that. You're a monster for trying to kill/killing them. But everyone else is fair game, hell we'll even give you more ammo to kill them with if you pre-order! It's like the game decides to ignore it's message for most of the game.

Generally it's an issue with the tonal dissonance with the rest of the game. That not only does Ellie kill her way through the game for Abby, both named-characters and nameless mooks, that it's also a character shown to be borderline psychopathic and dangerous.

If killing Joel was Abby's only real crime, it'd at least have more weight to it. But even then, the trail of bodies left by both people leaves the decision stupid anyway. In-universe the people Ellie has killed in both games are still real people who are just in her way, but the one who actually hurt her in so many ways is let go? Kind of stupid.

Sort of like modern Tomb Raider trying to have Lara Croft act traumatized when she kills someone, only to have her massacre scores of people in-game anyway.