Well, Karin is for sure a main character as she is taking over Sakura's position. Sakura, although being replaced, still has an important role as the benchmark for Karin's replacement. Then, other characters in their shared universe who interact with either of them could be main characters too. For instance, Naruto could be involved, seeing as he is friends with Sakura and may have some sort of reaction to Karin replacing her. Also, characters from their respective teams or groups might be main characters as they would be affected by this replacement.
Karin and Sakura are the central figures here. Karin will be the focus as she steps into Sakura's shoes. But we can't forget about Sakura's friends and comrades. They might be main characters as they deal with the change. Also, any antagonists in the story who might take advantage of the confusion or upheaval caused by Karin replacing Sakura could also be main characters. It all depends on how the fanfiction is written and what the author wants to explore in this scenario of replacement.