This is an issue more with commercial agriculture. With plows and tractors in wheat fields and the like, you're killing lots of animals. That's just the way it is.

Here's an article discussing the issue: https://sci-hub.se/10.1007/s10806-018-9733-8 (Fischer, B., & Lamey, A. (2018). Field Deaths in Plant Agriculture. Journal of Agricultural and Environmental Ethics. doi:10.1007/s10806-018-9733-8 )

With a home garden, I don't know what the situation is in terms of animal deaths. Probably much less.

However, I have a brother who has a very extensive garden. He's very much hindered by "varmints" getting into his garden (raccoons, rabbits, field mice, some burrowing animals) and really destroying his yields. He's tried all kinds of things (traps, shooting them, big huge fences, even going a bit underground with the fencing) and it helps, but it's still a problem. And while it's a big garden, it doesn't provide anywhere close to all of the family's food - it's probably about 10%, just their fresh veggies.