Billions of invertebrates and other small animals are killed during tilling before planting, with pest/weed control during the growing season (even with "organic" or "natural" compounds), and of course during harvest.

This is inevitable, planting requires controlling soil and plants, and this will inevitably kill animals that you don't even see. Do you really think you can pull a weed without killing any of the invisible animals living on it?

Fishing/hunting also kills animals, but you can catch a fish or hunt a deer without restructuring an entire ecosystem. Which means you can feed yourself without killing quite so many animals.