Kakashi did not kill Rin rather she chose to die in the hands of Kakashi. When Rin realized that she has been made a jinchuriki of the three tails and that this was all a plot to destroy Konoha, she asked Kakashi to kill her. But Kakashi refused it by saying that he promised Obito to protect her.
In the next scene we see that the Kiri-nin are clearly disappointed by the fact that Kakashi killed Rin, one of them says "Damn it! He did it!", and another replies "After all the trouble we went through to get her!" But I don't understand why he had to kill her, why they couldn't wait, e.g., for reinforcements to arrive.
Obito Uchiha, even though crushed under the rock near Kannabi Bridge entrusted Rin’s safety to Kakashi. But, unfortunately Kakashi couldn’t protect Rin and even ended up killing her. But, why would Kakashi kill a comrade after witnessing Obito’s tragic end? Something isn’t right here, isn’t it? let’s dig a little deeper! Why did Kakashi let Rin die?
But, why did the Mist shinobi kidnap Rin? You must be wondering right? Let me tell you, why! The Mist shinobi were controlled by Uchiha Madara using his Sharingan. He made them kidnap Rin and seal Isobu (The 3 tails) inside Rin. Wanna know why? He did this to get Obito to the dark side and make him a part of his plan, project Tsukyomi!
Kakashi kills Rin - Rins Death - Kakashi and Obito Unlock Mangekyou Sharingan.
Rin committed suicide by throwing herself in front of Kakashi when he was about to use Chidori on a enemy shinobi. She did this with good intentions; she gave her life to protect the Leaf, because she was being used to transport the Three-Tails to the Leaf village so the beast could destroy it.
I don't think kakashi would kill Rin to awaken the MS, because he did promise obito to protect Rin so I don't think that kakashi would do it for that reason. I'm pretty sure that that was the real kakashi that killed rin too, because of his reaction when obito said "because you let rin die" he showed sorrowful face.
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Rin's death, much like the deaths of every person dear to him, affected Kakashi but more so than usual since Rin had loved Kakashi and had also used him to kill her with his own hands. Even on the verge of death himself during Pain's assault on Konoha, Kakashi lamented on how he failed to protect Rin and said he was going to see her alongside ...
It is still a spoiler - Anime viewers know that Kakashi killed Rin, but the reasoning will not be revealed yet. They're currently at chapter ~619-20, and the explanation is in chapter 629. permalink