That's still making assumptions based on our human understanding of the cosmos. Our "laws of physics" could be a localized understanding in our region of space, and much, much, much more powerful entities could operate outside of that, where our perception of time and scale does not meaningfully apply. It would be near-zero cost to destroy potential threats, so they might as well. It's like humans eliminating pests and pathogens. It's standard hygiene, a low cost preventative practice. Nobody is targeting a single bacterium, they're just wiping down dirty spots. It's an interesting concept in the book because of how imaginative it gets with scaling.