Queen of Fables didn't make Harley kill any civilians. She was just a member of her crew who happened to kill some civilians during a job. Like King Shark. And Harley briefly re-teamed-up with Joker who killed Howie Mandel, a "civilian". She has no problem keeping Riddler around after he killed all those "civilian" university students. Her "line" is meaningless.
Yes, the writers are very careful not to show Harley killing any "civilians" on screen, but the line that they established isn't just for her, it's for members of her crew.
And if we go by things she said that happened off-screen, the "people in her way" that she killed when Gotham was in anarchy could very well be "civilians". I'm not saying that they are - maybe she's pure - but logically that's what will happen if a "civilian" gets "in her way".
That's why her entire spiel about her "line" - which was the focus of an entire episode and more - is bad writing. She doesn't really have a line, and whatever Queen of Fables did wrong, other members of Harley's crew did too (King Shark, to a lesser degree Ivy), and killing "people in her way" or "unintentionally" can result in killing thousands for no reason >>115201141
which, by the way, is pretty intentional even if you try to spin it as "unintentional". She had control of a demon army and she sicced it on a city full of civilians, what did she THINK is gonna happen?