I like your theory very much but I guess we'll have to wait till next week for 606Madara did set up that incident.
1. Zetsu did said that Madara choose Obito. Madara can move in and out of the Uchiha (Leaf) village.
2. Those shinobi from the Mist were ANBU as they put on the mask. (like any ANBU in all Village).
3. Madara ensure the target was Rin, so that Obito freak out, and immediately the MS was activated.
4. Because Madara need Obito, and the team consist of Rin and Kakashi.
5. Because Minato was not there, and that was why Madara choose this incident.
6. Mist ANBU was order to get Rin body.
Madara's objective was get Obito to his side, and killing Rin (Obito's loved).
So whether Rin was spy or not, that was irrelevant.
Rin body cannot allowed Kakashi to bring to the Village to investigated....
anyways I have my own theory about Kakashi's MS because he is not uchiha he needs to train for a few years and increase his chakra status in order to use it properly and not to mention Kamui