Intelligence isn't the important factor there - consciousness is. Does it feel like something to be those entities in the simulation? If yes, then I'd argue that ending the simulation is like killing a person painlessly in their sleep.
I personally don't think ending the simulation is even the most troubling part. We could unintentionally create a simulation that's effectively a hell and then populate it with entities that have subjective experiences we don't realize exist. The only thing worse than ending a life is creating one just for it to suffer through its entire existence.