I think, since the new generation always surpases the last, and Naruto has a tendency to learn incredible jutsu in a fraction of the time it takes or took the previous generation, that kishi has set up the perfect conditions for Naruto being able to use sennin mode right away and kill a very weakened Pein with no problem. It's definately NOT out of the realm of possibility. I agree with you though. I think it would be most believable if Naruto comes, beats up a couple Pein's and then the rest of them, including Negato, leaves to regroup and rest up. It's going to be a serious shock to Pein/Negato that Naruto isn't afraid of him.. especially since he's got a pretty huge "god complex" thing going. ....1.) Pein was strong enough to keep people in order in Akatsuki. He also killed everyone we've discussed who were quite powerful.
2.) Sage mode takes time to master, yet Naruto did it in a matter of weeks-months (not sure about how time passes in the mountain, but let's assume it's flow is equal in rate to the external world.)
Those seem to be the two main objections to Naruto coming back in full sage mode immediately destroying a body of Pein. Naruto learned sage mode quickly.
Whenever anyone learns jutsu in Naruto, they do it quickly since we the reader have better things to do than wait and watch training for years. Sure it's OK to say it took Jiraiya years since we weren't watching.
One only needs to say that we don't know Naruto's strength now, and this ends. We judge on actions, we speculate on other matters. Right now we speculate on Naruto's fight with Pein. I'd like to see what he can do first.
But..... what if.... well... this is seriously a long shot.... but... what if Naruto does beat the Peins up to the point that Negato has to face Naruto and instead of killing Naruto outright he is able to see into Naruto's past or Naruto is able to make him understand the PAIN he experienced as a child too... that he can understand in some way what Negato is feeling... kind of like he did with.... well everyone... and that is what reaches Negato and stops him... am I being way too naive here???