And Pain seeing the attack coming and preparing for it is out of the question here why? Kabuto, an opponent much weaker than Orochimaru, survived. Do you think that Orochimaru would have died from a Rasengan hit, prepared or not, also? Pain is stronger than them both.
Raikiri is an assassination technique, Rasengan is brute force. (I love internet analogies) A gun is stronger than a knife, but if a knife pierces the heart, and the gun shoots the knee cap you will have staggeringly different results.Remember the Raikiri that went through Zabuza and Kakuzu? Rasengan is stronger than that.
People can get lucky but this was certainly not that, if Pain can't see something so simple coming then he has no chance vs Naruto, sage mode or no.Is not about being a "kid" is about the technique the kid used, if a "kid" shots you with a shotgun you would die yes? never mind that he`s the grandson of a sniper.
Also, the puppet Pain survived for quite some time with half his body missing. It seems disingenuous to assume one blow would kill Pain.