First off 448 redeemed Naruto's character in my eyes, it's not that he doesn't want to kill Nagato, it's that he wants to live up to the insane standard Jiraiya set for him.
I have three general theories, one of which I would hate with a passion (though it's unlikely) and two I think would help finish this arc and build the next main arc respectively (if one can ignore the fight between Teams Hawk and Samu as a "main arc).
1) Nagato kills himself to ensure Naruto CAN become Hokage, as without this, it would cause him to become very unpopular with the villagers and simply speaking his body is ruined and his and Yahiko's legacy can be entrusted to someone with faith, something Nagato lost.
2) Madara kills Nagato. Why? It hypes him, for the first time, as an evil ne'er-do-well rather than a questionable immortal. The story of the founding of Konoha seems biased and incomplete, but if it is taken to account (as we should, to the points where it is contradicted by other parts in the manga), the Senju usurped power from the Uchiha completely. This gave us a sort of sympathy for Madara, so this would at least keep Naruto's hands clean and would lead to the much anticipated final main arc.
3) Naruto is given the Rin'negan by Nagato. This one I believe is not very likely, probably 1/100, as Naruto is already given a lot of insane powers, mainly the Kyuubi and Senjutsu and Kishimoto really spaces power-up's well from what we've seen so far I think. It took Naruto forever to get Rasengan, FRS and Senjutsu, while we say a similar case with Sasuke though he was not given as much time on "screen." Anyways, probability aside, I think it ruins both Nagato and Naruto if it happens.