Naruto CAN beat Pein
Firstly, consider Naruto's Rasenshuriken ( RS )
The RS was analysed by Tsunade after it was used on Kakuzu, and she discovered that it destroys the opponent on a cellular level.
Now, consider Pein's abilities
He controls dead bodies via a series of chakra receivers implanted on them. These receivers are obviously not just stuck on, but dig deep into the face of said body.
So, what do we have? If Naruto uses his RS on a Pein body, its cells near the chakra receiver will be destroyed, leading to the dead body becoming - a normal dead body.
Sorry if ive duplicated a thread.