Dini, Harley's creator, talks about 35 secs in.
Essentially Dini was creating some henchmen for the Joker, then on a whim he thought about making one a female, then he started imagining his friend Arleen Sorkin as this character, then he remembers she essentially played this type of thing on Days of Our Lives, then he literally bases the two tone design of her costume from that episode.
Whether he started down this line of thought to avoid the Joker jumping out of a cake, I dunno. It was serendipitous however as Arleen was available and a comic icon was born with her performance.
Edit in: Harley's gnarly look they use in the film and modern comics just may have been lifted from Alice Cooper, I dunno. Originally she was designed in a very classic way to match the original Batman four color designs.