Yuyuko wasn't aware of the tree's effects or the truth behind it when she went about doing it. Her plan was more ignorant of reality than evil.
Even Okuu wasn't evil for long, after she gets beaten, she's back to the egg loving birdbrain she was before.
Actually, Okuu misunderstood the whole concept of nuclear power from the very beginning. It was given to her by Kanako with good intentions, to move Gensokyo forward with modern technology, and also to make underground a livid place again, since it was forgotten and abandoned place for everyone banished (oni, tsuchigumo, satori). Of course Okuu the Birdbrain hadn't grasped the whole idea, thinking of her power as a way to take revenge on everyone at the surface. Much like in our world it can be used as either huge energy source or a terrible weapon.
Or maybe I'm just misunderstanding the endings, but the whole story makes a lot of sense this way.
