You might enjoy the philosophy Masanobu Fukuoka, who advocates for "do-nothing farming".

[0] https://en.wikipedia.org/wiki/Masanobu_Fukuoka

[1] https://en.wikipedia.org/wiki/Natural_farming

I think of it like combing the tree's hair. A tree sends out branches in all directions, but many of those branches are growing towards branches that are already there where the sky is already shaded. Many of them will naturally die off when they can't find enough light.

We're just expediting the natural process and opening the tree up to the air and light. Ultimately, we're saving the tree from investing energy into dead ends and guiding its energy into the branches that can most effectively reach more open sky, which is what the tree really "wants." We're just acting as the tree's eyes to guide it.

Pruning plants is very often good for them.

You have to remember that in the "natural world" (whatever that means), trees are damaged all the time by browsing animals, falling limbs of older trees, intense weather, falling rocks, etc. They and their ancestors have evolved under variations on those conditions for millions of years, and as such a lack of those things in a controlled garden or suburban environment is an unnatural way of growth.

Our (imperfect) knowledge and judgement can allow us to, rather than provide an environment totally lacking those natural events, wisely prune trees in ways which help them grow stronger than they otherwise would. Although you may intuitively feel a certain way, feelings are sometimes wrong.