Kirin needs thunderstorms to accumulate so Sasuke can use the tech. So, Pain would have to ignore the chakra build up and Sasuke utilizing the storm clouds (which the Rinnegan can see chakra manipulation). Also, Nagato does have that tech that can blow clouds away...Shinra Tensei. *blows the clouds away, no Kirin*. Plus, he could activate a Shinra Tensei shield to block it.
By the way, science equations are negated when human beings, in an anime, are spouting flames out of their mouths and flying...