That's the thing about Harley and "recovery" - most of the time she believes that somehow, she can have it all. But when she's rehabilitated the fact that Joker can't love her the way she wants him to - so that she's enough for him - is the cause of a lot of conflict for her which subsequently means a denial of him. She's trying to play by everyone else's rules.
He does love her - that's subtly made very clear in both these stories - (note how he grumbles she hasn't come to visit him) - but he's a selfish, egotistical, cruel being who will never ever compromise - so if Harley really wants to be free and live a normal life, he has to go.
Of course, she doesn't REALLY want to live a normal life - Harley's priority here is really freedom and she cycles in and out of thinking the path to freedom is rehabilitation only to go back to thinking it's actually a criminal lifestyle. Plus she just can't give up Mistah J.