I know it's absurd but somehow I've always intuitively felt that this sort of gardening philosophy (and especially bonsai) is cruel to the plants. It's like we're forcing the plant to grow in an unnatural way by abusing it.
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.
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.