Really, it all depends on how, at the moment, she thinks she can best help him. After all, that's why she got into the business of psychiatry in the first place – to help people. To improve the quality of life of people that everyone else had given up on, to reach out to the lowest of the low, the sickest of the sick, and give them one tiny ray of hope, of happiness, to show them their good qualities (Harley believes everyone must have some good qualities, even the Batman, though she hasn't found one for him yet), and give them the potential to be something more than they are right now.
But somehow, with the Joker, her desire for his happiness overrode everything else. She's not sure how it happened. (The Joker knows exactly how it happened. The Joker had her pegged from day one.) But now she knows that her role in life, everything she's done up to this point, her very reason for being is to help the Joker. Because that's what she always wanted to do. Help people. Nothing has ever been, could ever be, more fulfilling.
But Harley's way of helping isn't always the Joker's. Sometimes she messes up, a wrong step, a bad joke, poor timing (timing is everything in comedy), and he gets mad. He gets so mad. And then Harley gets hurt. And at those times she selflessly realizes that it can't be good for him to be so mad, so violent towards someone that loves him that much, and she becomes one of the good guys. She sheds the harlequin costume and the white paint, and she goes to the Batman, or Gordon, and she lets them know where the Joker is. What he's up to. So he can relax in Arkham for a few weeks, recuperate, maybe even attend a group therapy session or two (she remembers fondly the ones she used to run with him – oh, he was so cooperative! So insightful and willing to discuss his problems!) and then he'll be refreshed and ready to go. And this time, this time, he'll truly love and appreciate all she does for him.
It's all for his own good.
Notes: This fic was inspired by the comment_fic livejournal prompt "Harley wants to be one of the good guys." I'm not sure how well this fits that prompt, but it's what I wrote. I really enjoyed writing this because I'm a psychologist (not a psychiatrist) and it was easy to channel my motives into Harley's warped ones. Plus, I don't know anyone who, early on in their therapy career, didn't encounter an unrepentant sociopath, and yet found themselves being charmed enough by them and liking them enough that they convinced themselves THEY were the ones that could help this person. It's practically a rite of passage. Harley just didn't survive it.