We're currently in the midst of a mass extinction which is largely being driven by humanity. The selection pressure that we are placing on many species for outweigh's natural selection's ability to act on random mutation to promote fitter variants.
What you are promoting isn't a course of action that will lead to an alternative, rich ecosystem better suited to current conditions. It would simply lead to an impoverished and more fragile ecosystem, ultimately less capable of supporting humanity, if we want to go down the reductionist utilitarian road.
We are custodians of an astonishingly rich and diverse biosphere, which we are already damaging. We have a duty to try and mitigate that damage.
"Evolution" is whatever is happening - survival of the survivors. If humans kill a certain number of badgers and the number of hedgehogs rises plus a bunch of other hard to predict things happens, it's "evolution" as much as humans having killed larger predators and done nothing about badgers and whatever happened next. An alien observer might comment that the number of badgers went down due to humans, or instead that the number of hedgehogs went down due to badgers. The only real question is whether you think more harm than good is done by reducing the number of badgers, and it ought to be answered on specific grounds.
And I don't see why we can't keep regulating nature.