Okay, around the episode where Kagura is captured (because she tried to run away), Kanna is telling her that they cannot defeat Naraku, so it seems Kagura AND Kanna wish to be rid of him. However, around the ending Kanna is intrusted with the job of keeping Naraku's baby safe and hidden (no he does not marry anyone, another clone of him). This baby is special because the baby is Naraku's heart. Kill the baby, you kill Naraku. So if Kanna wanted to be rid of Naraku, she could have killed the baby and it will be the end. But she does as she is told enstead, so to save the mystery: Kanna is on NARAKU'S side, not Kagura's or anybody else.
Submitted by Shiro Ryu