Girls can and do like villain characters. But it's confusing for children in this particular context because for the past few years, DC Super Hero Girls went to great lengths to rebrand Harley, Ivy, Killer Frost, etc, as super heroes. Dolls, merchandise, clips, etc, all promoting them being nice and helpful and such good heroes! Get your cape on!!! ... no literally, buy dress up costumes to be Harley and Ivy and pretend to save the world.
Now they're villains. I doubt they'll be black and white characters--isn't part of the plot that Wonder Woman finds out her friend is Harley Quinn and she tries to reconcile it? unless they're removing that element--but in terms of branding it'll be confusing for kids. Especially since Harley and Ivy will be pulled from the core merchandise they used to be part of.