No, it hasn't been confirmed scientifically or otherwise. To "prove" that, you'd have to do one of two things:
To show that it is valid from an analytical standpoint.
To demonstrate that it works in practise and then draw conclusions about its validity.
Because we're working with humans rather than simple systems, an analytical approach isn't possible. Teams and organisations cannot be formalised.
On the other hand, empirical research have been carried out, but the results are inconclusive. In his book Software Creativity 2.0, for example, Robert Glass presents some intriguing findings.
So, no, agile hasn't been proven. That's not even close. :-)