There was a similar situation where Hank's former boss resigned/was fired after Gus was killed because he and Gus were friendly. Hank has to realize how bad it would look if people found out Heisenberg was his brother in law and had been making meth under his nose for all this time.
Just speculation but I think Walt finds out Hank knows who he is and that's why he takes it on the lam.
IIRC, he seemed to be somewhat reconciled with his family in the last episode. He and Skylar seemed at peace with all the money in the storage locker and he seemed to be getting along better with everyone at the party where Hank saw the book.
I don't know if they want him to be re-humanized, though. They have been making Walt more and more unsympathetic as the show has gone on. They don't seem to be giving him any moments where he becomes sympathetic as they did with Tony on the Sopranos and Don on Mad Men. That doesn't seem to be the case with Walt as of yet.