For instance, the Civ games are basically Whig History: The Game, presenting liberal capitalism as the ideal end point for all societies. It even includes uncivilized "barbarian tribes" whose sole purpose is to be exterminated so you can take their land for the glory of capitalism.
This is a good point. Though if my memories are correct, I do remember one example of the opposite of this, or at least in one of its game. The Walking Dead by telltale has several moments where key characters - sometimes awful, sometimes close to you - have been infected, or supposedly so, and you're given the choice to either kill them or having some compassion and being cautious. Of course this isn't that much better tbh since there's obviously a "correct" choice, but I do think there's some emotional weight to it compared to most zombie games.
Yeah the problem with putting that choice in the hands of the player is that the player has a pre-existing ideological foundation for what to do in a zombie scenario. The player has been taught by the vast majority of the genre to kill them without mercy because any kind of mercy or hesitation gets people killed.
And we're not even getting to the issue that zombie games reinforce the need for borders and walled societies, reinforce keeping even good people out because they might be infected, and reinforce the idea that the entire of humanity(now zombies) is an enemy, that the only ally that exists is your small society with hard borders and men patrolling the walls with guns. It is you and your society vs the world. It reinforces fascist ideology.