Naruto is not the type just to go awol just for a disagreement with the Hokage. He wouldn't just leave the village just for the heck of it like Sasuke did and leave the village in Danzo hands. He know what kind of damage Danzo can do. So he wont leave.
I know he a manipulative b**tard . So, this might be away too give Sakura her arc, and have her save Naruto from Asukti like a fan fic did called In your arms by Catsi356.
See, I believe that Danzo would arrest Naruto and then give him to the asuktai in return for keeping his village out of their view. Then Sakura and the Konaha 12 and team Hawk goes and rescues him.
Then a few years from know Naruto is Hokage and married to his lovely wife Sakura heee.
Naruto would not allow Danzo to arrest him, If that happened the Rookie 12 would take action and in the end he'd end up having to leave anyway. Have you forgotten, his made a promise to his godfather and Negato that goes beyond the walls of Konoha, He wants to end the fighting, for there to be peace amonst all villagers not just Konoha, If he allow himself to be arrested he's failed.
I'm pretty sure Danzo views Naruto as a secret weapon for the village, right? Then he may try and keep Naruto from leaving, like they tried a couple arcs ago. I really have no idea, I can't see Naruto leaving the village behind over Sasuke, but then again....
Guess we just gotta let it play out.
True Danzo see's Naruto as a weapon, but he also see's him as a major threat to him, Everyone knows he wants to be Hokage, so is a threat to the postition he worked his entire life to get into, also Naruto is the worst possible weapon for him, he's one who was created with the ideals of the man he dispised more than anyone, the Third Hokage. He's also the Son of the Fourth, As well as Apprentice to Jiaraya, and the one responsible for bringing Tsunade back to the village (and it's well known Danzo dispised the First Hokage's thinking too.) So he might realise that he won't be able to use Naruto for his purpose as a weapon and try to discredit and have him eliminated instead, he might also argue with him eliminated the Akatsuki can no longer complete their plan and having Naruto Dead gives them an instant win.
As i've ben saying I don't see Naruto leaving on his own accord, but it's entirely possible he has no choice in the matter. He's the strongest Ninja they have yet he's not killed anyone, that's a policy that directly conflicts Danzo's way of working, he doesn't like someone or they are opposing them, he'll want them six feet under, He allied with the enemy to kill Yahito because he was a threat. That showed how shroud and heartless he truelly is. He's basically the type of man Naruto cannot work under.
If you read the spoiler he'd probably already be in trouble with the Hokage if not for Kakashi stopping him.
ll that said, I don't think Naruto will be leaving the village but if for some reason it does happen I can see plenty of avenue's Kishi could use to make it plausable.