It goes without saying that the Joker has done some truly reprehensible things to Harley Quinn. He's warped her mind, abused her both psychologically and physically, and imbued her with an occasionally questionable fashion taste.
But, mercifully, Harley has also gotten in a series of pretty good jabs at the Joker during her time in comics, even if they were significantly less traumatic than her own personal suffering. While it might seem weird that the bad things she does to him are kind of justified, it's worth remembering that doing a bad thing to someone who deserves it is still a bad thing. And if there's anyone who deserves their comeuppance, it's the Clown Prince of Crime - so who better to dole some karma out than his long-suffering sidekick?
You can only imagine the likes of Jason Todd, Barbara Gordon, and anyone else mistreated by the monster jester would get a kick out of knowing that the person he hurt for the longest is also often the one getting the last laugh.
And she's managed some good ones over the years. Although Harley can never entirely get rid of the damage the clown did her over the years, she can kill his doppelgänger, steal his face, and shoot him with a sawn-off shotgun - which is a pretty good start.