Humans evolved in the same environment as the ecosystems we're modifying. The buildings and cars and roads we make are made of materials we find on earth, similar to how birds build nests or ants make anthills. (Whether all the things we build are good and healthy for us and our environment is another story.)
My hypothesis has long been that this view of human activity as "unnatural" was actually born of the religious perspective that some religions hold that humans were implanted into the universe from the outside.
> Instead, spend that time understanding the current system deeply, then do the simplest thing that could possibly work.
I'd argue that a fair amount of the former results in the ability to do the latter.
There's a substantial amount of wisdom that goes into designing "simple" systems (simple to understand when reading the code). Just as there's a substantial amount of wisdom that goes into making "simple" changes to those systems.