I doubt the thoery that is was only a Zetsu clone. If that is true, then Rin should be alive and Obito would know about this, and we could see Rin dillydallying on Konoha.
I have a hunch that Rin was betraying the leaf in some way, and there was no other choice but to kill her. Madara probably know about Rin's deeds for some time because he has information gathered through the Mazo which is connected to different places, but Madara refused to tell Obito the truth, and Madara knows that the fight was actually between Kakashi against Rin and the mist ninjas, which is the reason why Madara was confident in saying that Obito will come back to him, because Madara knew that Kakashi will kill Rin for some sort of betrayal.
Or it could also be an accident that he Raikiri'd Rin.
Well, just a hunch.