The RPG trope of forcing the player to make morally dubious choices in favor of quest rewards or following orders.
As opposed to a genuine moral dilemma, the "best way" is always a bad choice, but often masked as "lesser evil" option.
The effect of adding this in game increases doubt and creates emotional discomfort in the player's mind: this can be good for immersion, but long-term such choices will change the reputation of the game.
A lesser-evil choice is similar to philosophical "Trolley problem"
A moral dilemma like Trolley problem explores ethical consequences of clearly defined rigid actions, but quest lines may hide information(incomplete information game) and NPCs may lie to the player.

RPG should avoid any such hard choices in the RPG unless its explicitly the theme of the setting(e.g. Dark Fantasy, Gothic Horror,Psychological Thriller,etc), most RPG players are there to play for fun and tactical challenge,not solving multi-level Trolley problems.
Alternatives to moral ambiguity is create a clearly defined moral system in the game("law and order", right-choice vs bad-choice) and/or presenting choices as path to different alignment(clearly outlining their effects): see