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.
I know. I'm responding to KEyes suggestion that Naruto can call out KB's chakra even if KB itself was under control (or something like that, I think?).

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.
Regular genjutsu, sure. But Sasuke and Madara both know about Naruto's Kyuubei, and they both have the Sharingan. I'm proposing the possibility that they can cast something at the same time that would screw up both Naruto and the KB.