Choice & Consequences is a meme propagated by people who can't be bothered to play RPGs released before 1997 and who lack familiarity with
Choose-Your-Own-Adventure books or the
gamebooks that combined RPG elements with CYOAs.
Computer games are singularly unsuited to providing narrative C&C relative to pen-and-paper RPGs, and complexity of game mechanics is the true C&C.
Oh yeah, cause 80s CRPGs had no Choices and Consequences. None whatsoever
C'mon bro, that is a slippery slope, if this is C&C then literally any decision in-game is C&C, stealing a car in GTA is C&C cause you had the choice of not to, now a random generated NPC have no car. fighting a battle in a JRPG is C&C cause you could've run from it instead, now you have more blood in your hands. Jumping on a goomba in Mario is C&C cause you could've jumped pass him instead, you monster. While all actions in a video game are a choice and have a consequence, even starting it(you had the choice to click Exit instead of New Game), we need to draw clear lines so it does not end up in a meaningless slippery slope term.
For me C&C are distinct choices that feels meaningful, that's going to have long term consequences for your gameplay or that's going to change the game world permanently, or story. Emphasis on distinct, choosing your own build in a RPG, strategy/playstyle in a Strategy game or taking your own path in a story/campaign, needs to be distinct enough and have long term consequences to be considered C&C. I don't think Half life or Call of duty and others linear games have any C&C, yes each playthrough of someone is going to be slightly different, some are going to die more, others are going to be more efficient, but not enough to count(we are against slippery slope here). Same with your example, not killing a random encounter of friendly flies is not a meaningful choice, neither consequence(unless i'm missing some context here), neither is choosing to kill or not the scientists in Half Life.
The more freedom a game gives to the player to make each playthrough and playstyle different the better.
I do think almost all if not all RPGs have choice and consequence, since almost all of them have some kinda of character customization or story path that can feel distinct enough to worth a replay. That does not mean all C&C are equal though, choosing spears instead of axes is not going to make the game as distinct as choosing another faction in Fallout New Vegas.