Honestly, this is one of the biggest problems I've found with comicbook Harley Quinn in general, not just because of her hero turn.They wouldn't go THAT far...they'd just find some way to blame it solely on the Joker, and instead of gleefully participating she'll have reservations of what Joker is doing, and gets forced to participate.
In the cartoon where she came from, Joker was far more an eccentric gangster. There was a lot more fun in what he did. It's easier to overlook the bad qualities in a guy that's just out having a good time.
Comic book Joker, by the time Harley had gotten introduced was already at the level where killing an bus load of orphan and bathing in their blood wouldn't have been out of the norm.
It's hard to see how Harley would have ever thought he was a good guy deep down and even harder to forgive her for going along with him.