The Ninetails has shown in the past that it can act completely without input from Naruto. Like when Sasuke broke his neck in part one. He was basically dead, but the Ninetails stepped in anyway.
Genjutsu usually just effect the flow of chakra in the users brain, since the Ninetails is down in his stomach, he should be able to send a chakra surge to break Naruto free.
I'm STILL dying to know what Itachi implanted in Naruto that one time. It would be awesome if it just, like, broke Sasuke's Tsukiyomi when he tried to use it on Naruto.
Knowing Shounen anime though, it'll be a spirit projection like the kind the 4th left inside Naruto that will come out at the climactic moment and say something profound that will get Sasuke to see the error of his ways.