Holy crap, there's SO MUUUCH BLOOOOOOD~! Obito massacred those Mist ninja, holy crap, he scares me now. And he can use Mokuton now, that's interesting. Makes sense though; he has Hashirama's cells, and Zetu's probably helping him channel it. I still think Madara's involved; not in killing Rin or anything, but getting Zetsu to fuel Obito's rage. I bet Zetsu has some measure of influence on Obito's mind at the moment, he's pretty much supplying half a brain for him.
As for Rin; Kakashi said her name after she fell over, he seemed really sad about it. Here's my theory; Rin had information the Mist nina seriously needed, and she could tell that they were gonna get to her and force it out of her or read her mind or something, so she asked Kakashi to kill her before they could get it. I'm convinced now that Rin's name is on the memorial stone as well as Obito's; after all, she died in battle for the Leaf Village, KIA. Kakashi visits the stone for her as much as Obito.
That also explains "You let Rin die" rather than "You killed Rin". Kakashi wasn't able to protect her to the point where the ONLY option left was to kill her. From a certain point of view that could be letting her die.