But they would cease to exist. If they ran it to its end, then it's over, they could just turn it off then. I mean, if you want to cease to exist, fine, but otherwise there's no reason. Plus, the topmost layer is likely very, very different from the layers underneath it. In the story, it says that the differences eventually stablized and created them, but who knows what it was originally. In other words, there's no garuntee that you even exist outside the simulation, so by turning it off you could be destroying the only version of yourself that exists.