Naruto did win that fight but its quite obvious that Nagato was by far the more powerful of the two. Nagato would have won the fight on multiple occasions if others had not interviened. Nagato fought the entire village before Naruto even showed up and it was Shima who did the summoning. I really don't see how it can be argued that Naruto was on par with Nagato at the time of their battle. Naruto won but the strongest person doesn't always win, that has been shown throughout the series repeatedly. It seems quite obvious that the situation was stacked against Nagato to make his defeat at that time realistic. It isn't all that different from the situation that occured between Sasuke and Itachi. Those battles where set up for Naruto and Sasuke to win because that is what needed to happen but based on the circumstances of those battles it is obvious that the ones who died were the stronger ones. That's just the way it is.