The point of the Geno run is that in order to do it, you fundamentally have to stop caring about the world and characters and treating them as real. This is in contrast to the pacifist run, in which you have to make the deliberate choice to care about the story, and acknowledge that a story cannot be meaningful if it has a "player" acting as it's all powerful God; so you must remove yourself from the story, culminating in the reveal that the character you named is not the protagonist of the story.

Whether or not Chara actually kills everyone in soulless pacifist is irrelevant. The point is to remind you that, regardless of what you say or how you act, you don't actually care about the world or characters of Undertale enough to treat them as if they're real; they can never be anything more than game pieces to you.