For all we know Naruto could still have went to go train in SM, Jiraiya would come back to Konoha to pass on this lesson to Naruto by taking him to the Toad place. Kakashi went on to train Naruto after hearing about Sasuke's growth so Jiraiya could decide to train Naruto after seeing what became of his first student (Nagato).
Anyways, Taka isn't taking down Konoha; there's thousands of ninjas in Konoha. Sasuke would have MS but he suffers pain whenever he uses MS jutsus and genjutsus, loses a lot of chakra, and his eye sight grows weaker. Naruto's base was stated to be on Kakashi level if not surpassing (Kakashi stated this) so Naruto can still pull off a win since this is still Sasuke after he attacked Bee but before he went to the Kage summit so he wouldn't have nothing but Amaterasu and Rib Susanoo which doesn't fully protect Sasuke from attacks all over, Naruto's FRS (50% completed) could hit Susanoo rib, explode, and do its damage to Sasuke which would kill him.
Kakashi takes down Suigetsu (lightning weakness), Sakura/Ino/Hinata/Tenten can each take down Karin, Neji can take out Juugo, and Naruto+Shikamaru+Sai+Lee can all gang up on Sasuke if he's too much for Naruto alone; Kakashi got backup fighting Pein when he couldn't finish it himself so something like that.