it's not much of a choice if there aren't any consequences. it would basically be larping, where all the choices don't matter and the consequences are imaginary.
also, this discussion is moot. the doctor is not that hard to kill if you had decided to snuff the candles and killed the vendor. the final boss is not that hard to kill, especially since all your source skills are free; in fact, i killed him in less than two rounds. i'm guessing not one single person failed to beat the game solely due to some crucial skill they needed from the dead vendor; this hypothetical newbie gamer just doesn't exist. if you made it through the arduous early fights in fort joy, then you can beat the game.
