There is a simple way you could do Harley without the Joker. The Joker's chaotic war on Gotham in the last movie had a profound effect on the city. There could be a young impressionable girl who viewed what he did and became obsessed with the ideals that the Joker embraced. This girl was inspired to take on a persona of her own and go out performing her own acts of chaos on his behalf. She calls herself Harley Quinn and her outfit is similar to the one that the character has in Arkham Aslyum/City the video games. She's a anarchist/goth chick.
Or if you wanted, you could have the more traditional Harley origin of her becoming corrupted by Joker and his ideals while interviewing him as his "counselor" during his incarceration in Arkham. There are a multitude of ways you could introduce Harley in the Nolanverse had he chosen to use her.