If the logic is obscure, consider passion as the motive.
Walt is the king of rationalizations. I think that in the end, Walt in effect murdered Jane because he wanted to keep his surrogate son. As it turned out, it was vital to saving his life while yet keeping him in business, as Jesse was his only ally against Fring.
Now it's true that Walt is and has misused Jesse with terrifying callousness. I suppose the worst was his misrepresenting the murder of Gale as the only alternative to the death of the (surrogate) father. But I think that Walt's fundamental brutality towards Jesse expresses his resentments towards Walter Jr. It looks as if the show is going to wimp out on really confronting the underlying issues, though.