This 'doesn't like' comment is not from Kishimoto, but from the interviewer, apparently. Kishimoto has said something that puts Sasuke on a nice literary pedestal. He basically says that 'Sasuke challenged him as a writer.' The 'he isn't obedient, and I had a hard time writing him' doesn't even remotely translate into dislike. Sasuke kept him on his toes. He didn't know how to write him easily like all the characters.
Funny, because that is the ultimate compliment Kishimoto has ever given to anyone, as this is what every writer dreams - a plot or a character that challenges him and brings out its complexity. I think I have gained some respect points for Kishimoto, as he gave himself a hard time to flesh out Sasuke.