How was it supposed to be batman killing the Joker when the story was actually in continuity at the time, and Joker was alive and well after the story? I'm also pretty sure the story was written specifically to be in continuity, not an elseworlds story that got put into main canon at the time, so obviously the intent wasn't that Joker was dead. I mean, maybe Alan Moore had it in his head that the scene was meant to represent that (although evidence seems to go against that), but from DC's perspective nothing in The Killing Joke was ever meant to imply that Batman killed Joker.
As for the movie adaptation, Barbara getting shot they'll easily allow, in Flashpoint they showed characters getting shot a lot worse, and they also had a decapitation. They might change a bit of the naked Commissioner Gordon stuff, but a lot of the story will probably easily conform to how much they currently allow the animated movies to show.