In Watership Down, humans are very often the ultimate enemy of nature: they poison warrens, they shoot rabbits, they trap rabbits, and they generally just kill rabbits. But this isn't just a book about what jerks humans can be to nature. There are also hints that humans and rabbits aren't so different: we both have social structures and politics and art. So perhaps humans can learn to appreciate and live in the natural world, just as good rabbits do (but also with computers).
In Watership Down, what's unnatural is always wrong, plain and simple.
Watership Down ignores the several real examples of humans living happily with animals, like the cats and dog on Nuthanger Farm. Harsh.