I really don't think Kishi will kill Kakashi by the end but I do think that he will lose his Sharingan eyesight by the end. He has gotten better control of it ever since the time skip but so far during the fight against Tobi/Obito, his eye has started bleeding because he has been using it too much. I think by the end of the war, he will have used it too much and his final Kamui, (just before he loses his sight), will help determine the end of the fight against Madara or will save Naruto against Obito.
good theory, kakashi is a non uchiha so i agree, I'm not expecting that eye to upgrade unless obito's eye got an upgrade, then his will judging from the fact that when he killed Rin he blocked out, maybe its because the link connections of obito eyes, since both of them achieve MS the same time. however it can also mean, he just over used the eye against the mist enemies, to counter there genjutsus, but by the time he broke free from it, he realize that he killed Rin, which could cause his, upgrade. obito's is similar, he saw rin got taken out and it drove fury and rage in him, to kill kakashi.
good point though kakashi can go blind, his stamina is already over so to speak, guy will have to use the 8th gates sooner or later