What good did humans do? What exactly would you define as "good?"
Midgar be repopulated? It was completely and utterly destroyed. Maybe the humans left it there as a symbol of what can happen when power hungry bastards get control.
Ok, one last time: Humanity, you believe, warrants complete destruction. Why, then, were the Weapons not summoned to destroy them? Humans were a harm unto themselves, not the Planet. They only harmed the Planet when they started using mako reactors, but they were all destroyed. They aren't a total threat to the Planet now.