In context of sustainable ecosystems, I agree with your detailed explanation. Controlling and maintaining a complex system of feedback loops (that we still don't completely understand) is a very difficult task though, so I'm not surprised that currently the most crude methods (genocidal chemical warfare) are also the cheapest / most efficient.
I wonder if this isn't a good field to benefit from computational models though - from tools to design, predict and manage natural feedback loops in agriculture. I don't know, maybe it's already a thing in the industry?