There is a simple way you could do Harley without the Joker.
Yes, you could remove the Joker from her backstory entirely. I'm not sure if that really leaves her as a recognizable character, though.
The alternatives boil down to her being directly tied into and talking about a character who ain't in your movie, as I've observed above.
Given these facts, should Batman be violently opposed to, say, the State of Texas?
I'd assume Batman is against the Death Penalty, yeah. If he's involved at all politically it's something I could see him trying to repeal with that sweet, sweet megacorporation moolah of his.