Couldn't you argue that the show's message has always been this -- even back in season 1?
In Season 1 episode 1, Bullock asked Gordon to put a bullet in Penguin's head, but he chose not to do it.
How many people has Penguin killed because Gordon chose not to kill him? How many more people will Penguin kill when Bruce finally becomes Batman?
What about Batman's "No Kill" rule? The Joker keeps escaping Arkham, and keeps going on mass murder sprees, because Batman refuses to kill The Joker. How many lives would have been saved if Batman had just killed The Joker? You call it a shitty message, but that message sums up everything about Batman.
Batman has said that there can't just be one. If he kills joker he knows he won't stop.