This is really hard to answer because all discoveries give humans new powers and powers always have a dark side.

Ignoring the net benefit, I'd say oil. Mostly because it's the most powerful discovery we've made as evidenced by how much it changed our lives. It's probably given the most benefit and the most harm simply in terms of being a catalyst for nearly everything (good and bad) that followed.

I can't think of any discovery that doesn't have this duality and it's hard to measure net benefit. I wouldn't rid us of nuclear physics because we learned how to make bombs with it.