A movie can be an ensemble and still have a clear lead. In this case it's Harley. In the case of, say, GoTG it's Peter Quill.
I'd say it's more like Harley was being used to launch the other characters. She splits off from them at the end. The BOP were being set up as a team separate from her, they could probably have had their own movie spun off from this. It seems pretty clear if you watch the movie that that may have been Robbie's intentions. It sadly might not happen now, but even getting them in something like this without Harley seems like it would have been slim.
If we do get a BOP film sans Harley, Barbara (as either Batgirl or Oracle) can easily be added into the sequel. A BOP film franchise without Barbara is BAD, but this is more like a BOP back door pilot than a full BOP film. Her being absent for just this is hardly the end of the world, and Montoya, Canary and Huntress were done justice as far as their characters are concerned. Give the latter two some more comics accurate costumes (preferably the less male gaze-y ones) and we're good.