No, you're right that Kotori would have died anyway, if we believe Hinoto (she tells Kamui that all futures had Kotori dying, regardless of Kamui's decision, I think); but there's a great deal of interpretation. Why does Kotori die? Which is to say, why does Fuuma kill her? There's of course a great deal of mystery about why Fuuma (once Kamui of Earth) does anything, but we know he acts in accordance to people's wishes. Pragmatically speaking, killing Kotori makes him lose the time that allows the Seals to arrive, and thus prevents him from killing Kamui. So, I guess I read it as, having been warned by Kakyou about the future, Kotori makes the wish to be killed by Fuuma before he kills Kamui, so that Kakyou can use her body to prevent Fuuma from killing Kamui. But it's very muddled and a great deal of interpretation from my part.