There was always something fishy about her, and I believe she was the Sanbi jinchuuriki. Chronologically, it works out. The Mist clearly wanted her, and Kakashi had to go to drastic measures to make sure they didn't get her. What could she have been protecting? I doubt she was a spy, because she seemed genuinely kind to her teammates. Not only that, but Kakashi still mourned long after her death... if she were a spy he wouldn't be lamenting over her because she was a traitor. She only showed medical ninjutsu so I doubt she had a special kekkai genkai either. She also doesn't have red hair so she's not an Uzumaki (or at least there's a high chance of her not being one). So what else could she be but a jinchuuriki? It would make sense, because assuming that she did end up getting caught by the Mist, her jin would have been extracted and given to Yagura. This would lead Obito (under the guise of Madara) to hold a grudge towards Kirigakure. This would lead him to controlling Yagura and becoming the puppet behind the Mist. He is so angry that the greed of the villages would go to such lengths as to kill his friend over power that he wants to collect all the jins and support the Moon's Eye plan. Another possibility is that she was going to be the new host of Isobu, but the Mist didn't want it to happen. We still don't know anything about the 3rd Mizukage, so he/she could have been manipulated by Madara or even have been Madara himself. He extracted the Sanbi away from Yagura and it roamed free until a new host would be found. Rin was going to be the new host but Kakashi killed her, causing the Sanbi to roam in the lake until Deidara caught it. This is more unlikely, though.