Namine isn't a member of the Organization for one thing, and second she is a special Nobody...being barely made of anything at all. She has a tiny piece of Sora's body and a bit of Kairi's soul or whatever you wish to call it...essence of Kairi.
Nami mean "ocean wave" which definitely represents her character, having "pushed" her way into Sora's memories, sweeping away the memories of Kairi. Like Sephiroth said, it also fits into the theme of the main females having water-based names.
Kai (for Kairi) - Ocean
Nami (for Namine) - Wave
Shion (for Xion) - (sound of the) Tide
Aqua - Water