Kushina and Minato had Karin kept her birth a secret and decided to keep her hidden outside Konoha. After the Nine tails attack Kushina left Konoha because it was to painful to stay there after her lover died and she could have been told by someone that Naruto died. Kushina reaches where Karin is being kept and raises her until she runs into Orochimaru and he was one of the few who knew Kushina was Minato's lover so he decides to take both of them and raise Karin as his soldier and keep Kushina in a dark cell somewhere. Orochimaru would do this because of the hate that Minato was chosen to be Hokage over him.
Karin has red hair like her mother Kushina and she has a hyperactive personality like her brother Naruto. This could help tie up what happened to Kushina and a way to bring Kabuto back in the story since he would be the only one left who would know where Orochimaru kept Kushina locked up.
Karin could just be Naruto's cousin the red hair could come from one of Kushina's brothers or sisters. I feel there is more to Karin then a simple fan girl.