But why would it be bad to simulate humans in such a situation, yet it's fine to script a story where that happens?
The main question is whether hypotheticals are morally real, then. And keep in mind that (as far as I know) we can never rule out that we are living in a simulation ourselves.
We're certainly living in a hypothetical universe that is being simulated by an infinite number of hypothetical computers. But ours is special, as I'll demonstrate.
I'm now imagining a universe like
XKCD's man-with-rocks, except the person is a woman. Both these universes are now simulating our universe. There are infinite permutations available, all simulating our universes.
In fact there are universes simulating every universe, including permutations of our universe. Like in the comic, the man misplaces a rock - permutations like that, including the moon disappearing or the strong nuclear force ceasing.
If our universe is merely one of these infinite simulations, then the odds of physics continuing to work are statistically near zero.
If all conceivable, hypothetical universes had consciousness like you or I, then statistically speaking we should be experiencing total chaos. But we aren't.
Therefore, it's morally safe to imagine hypothetical universes, since the beings within are astronomically unlikely to have consciousness.
Even if they are otherwise copies, or near-copies, of us. Even if they react as we would, and it's natural to feel empathy for them.
We could definitely be brains in jars, but I reject the idea that simulation can create consciousness.
(This "proof" from my butt sounds familiar, I'm probably remembering something I read... Probably from some sci-fi growing up. I'd like to know what it's called, if anyone recognizes it. I really should study actual philosophy more.)