I doubt Kishimoto will have something to do with the side story, I know he did have something to do with the movie, but most of the time side stories in animes are made by people other than the author that have no talent.
As a result 2 things happen:
#1 they make the anime more confusing and even go as far as destroying the original character develpment that the author had.
#2 They become way predictable, thus people lose interest on the anime (Saint Seiya comes to mind)
Unfortunatelly there's no way to stop what's coming for Naruto, is either that or stop the anime for a while, and because Naruto is making some good $$ there's no way that would happen.
I'm just hoping they don't make the new saga like that "battle at something waterfall" special.