Character becomes famous for being such a psychotic masochist she can love a psychotic sadist....So someone has the brilliant idea of "emancipating her" as their big story line. Derp.
Harley works as a character because of her obsession with Joker. Even in that cartoon--the story only really works still because she's still clearly obsessed with Joker. Her being a strong, independent woman is just not what the character is. Its not what's interesting about her. (Frankly part of Harley's whole persona is she would die on her own--she's too needy and crazy.) If you change this, you fundamentally change her--and if you're going to do that, I have to wonder...Why make a Harley Quinn movie at all?