A friend of mine agrees with you about Madara controlling the Mizukage before Tobi. You've presented your point really well. Although some parts are unconfirmed, it has the smell of good sense about it. I'm sleepy though, so I might have missed something!
There was a theory which says Rin waas in fact controlled by Mist nins by genjutsu; so she wanted Kakashi to kill him. She was not a traitor i suppose, her grave is in Konoha.
This theory from Centipede might be an answer:
Best theory I heard was that Rin's eyes record things like a camera. When Kishi draws her eyes they have the same faded diagonal lines running through them that all the photograph shots in the manga have. So when Naruto looks at old photographs or Obito does the pictures are drawn to look like her eyes.
Even the way the Mist ninjas talk about her its like, "at least retrieve the photos!"
She was an unwilling spy that's why she's buried in Konoha