I don't like it either.
I think kishi see gai as his DAD and he protected him from death through naruto unlike the real world in which his father died.
Well honestly, kishi's dad's death should not effect the manga, but sadly it is.
Gai should have died totally, but its his manga, and manga is basically a way for him to express his opinions so if he wants gai(his DAD) to live , then whats wrong with it...
Miracles do happen , at least they can happen in the manga.
There is no logical explanation for gai not dying, just kishi's wishful thinking.
I just wrote this so that you can understand why gai didn't die.
I think u would feel less bad about gai not dying now.