If we go by what Kishimoto's assistant was saying... it seems like Kishimoto intended to make NH canon somewhere around the end of the Pain arc. SS came as an afterthought (as the assistant was unsure they would be together). He also said Sakura wasn't heroine-like... echoing exactly what the interviewer told Kishimoto a while back.
I guess those anti-Sakura comments really got to Kishimoto.
This gives me the feeling that he changed his mind because Sakura was bashed. That would be very awful.