I think she was *supposed* to die anyways. But the story is that Dini snuck her in at the end of the movie, giving her a happy ending and Bruce Timm ok'd it because they needed some lightheartedness. (There's even a drawing of the anguish Dini had over the thought of having to kill Harley somewhere...)
But yeah agreed on Joker dying due to misfortune being a bit off. I like the movie version of death better (shot by Tim with the bang gun).