|I'll put my prediction in spoilers, just to be safe. Completely unconfirmed, but it seems logical to me:
Spoiler (mouse over to view)
Rin was always a Mist spy. The Bloody Mist was known for using children (and Kabuto was a spy for Orochimaru around the same age). Plus, they seemed very interested in retrieving her body (which was a big thing discussed after Haku "killed" Zabuza -- they need to destroy the body to avoid the enemy getting village secrets and techniques).
I agree this was mostly a waste of a chapter. Although I guess I shouldn't complain about his instinctive use of Kamui the instant he gained it, because that was what happened to Nagato as a kid. He'd get angry and use his eyes instinctively to kill lots of people. It's still annoying though that with no additional training and a weakened body he can be better than Kakashi all of a sudden.
I mean, even one-tailed Naruto didn't have that big a jump in skill, and that was actually a new mind taking over.