There are interesting arguments here. That Kakashi being a Zetsu clone might be possible. Would certainly explain why the Zetsus at the cave, who serve Madara, were so eager to get Obito to the war site.

But although Kakashi did ask Obito "aren't you gonna blame me?!" I don't think it would make any sense for Kakashi to ask that if Kakashi had indeed killed her, cause it would obviously been his fault in that case. What Kakashi always said at the graves was "sorry that I couldn't protect Rin", like he wasn't there or wasn't strong enough to prevent it.

When I first saw that image, of Kakashi killing Rin, it reminded me of one of Kisame's flashbacks, when he had to kill his squad mates to protect information.

http://www.narutobase.net/manga/Naruto/507/10

Could that have happened to Kakashi and Rin? At Kakashi Gainden Rin is a Medical Ninja. But some time later, she might have come to be a greater asset for some reason, too great an asset to fall in enemy hands... Although Kakashi had swore to protect her, he also is strict when it comes to follow the rules...

Also, here we see Kisames death as a reason of pride on the eyes of Gai, Kakashi's rival.

http://www.narutobase.net/manga/Naruto/508/14

What do you think?