Two words: Quantum Causality.
It might be that the threat humanity poses has nothign to do with our firepower/combat ability or whatnot, but the potential for individuals with the ability to change circumstances--so much so as to even bring individuals from alternate dimensions or to reset existence until the ideal reasult (or the closest ideal result) is achieved. EG, humans have the potential to be a "Demon" that changes the fabric of reality.
For further reading and comparison:
http://en.wikipedia.org/wiki/Laplace%27s_demon (Might interest Gundam Unicorn fans, too)
http://en.wikipedia.org/wiki/Schr%C3%B6dinger%27s_cat (To Aru Majutsu No Index fans know this very well)
http://en.wikipedia.org/wiki/Unexpected_hanging_paradox (TAKERU THIS IS RECOMMENDED READING FOR YOU BEFORE YOU THINK YOU KNOW EVERYTHING)