No. Earth atmosphere isn't simply localized, it's globally interconnected. "Messing with" even one small section can have serious repercussions elsewhere (as we’re seeing with global warming).
Unfortunately, we can't harness the energy from tornadoes or hurricanes. The unpredictability of these phenomena (size, strength and location) makes it impossible.
Tesla thought about harnessing lightning. After all, an average lightning bolt contains 1 billion joules of energy! But, alas, that too isn’t feasible, as physics won’t allow it.