Shonen Jump does own the rights, but I imagine SP owns an interest in the franchise too. They would have to purchase the rights in order to animate it, to my understanding.
SP are have the licence to make the anime, they don't own the manga, Depending on the contract they could own a TV rights for all anime related to the manga, or it has a expiry date, it would all depend on the actual contract between both parties.
SJ would own the rights to the manga, though I really do not want to think them presuring Kishi to do this, but you never know.
Reason is simple, Money, however on which side we may never know. The thing about Naruto is that it is just as popular abroad as it is in Japan if not more so, something no other manga based anime can say right now, not even One Piece, so it could be SJ who put pressure on Kishi, thinking they could make more money on the international market through this ending, it could be SP who convinced Kishi that this is what the fans really wanted, and it would make them millions. Heck it could be his wife for all we know, or it could be his own decision, wanting to ensure he milked the franchise as much as he could so he could semi-retire..Whatever it may be, the underlying reason is money.
If it was the planned ending all along, we would have seen more good SS moments, some NH moments, we wouldn't have seen the dispair or Karin, at the very least we would have seen Naruto and Sakura resolved their feelings allot better than, 'you only liked me because of your rivalry with Sasuke facade.'