If you have an entire weekend to devote, then you could plan on babysitting in the coop for most of a Saturday and Sunday with a big water bottle. That HELPED (didn't fix the problem, but it got a LOT better) me with a mean girl. I stuck a seat out in the run, took a book, and made myself comfortable. Every time she'd start stalking, I'd start squirting her in the face. My hope was that, since the streams of water appeared to come out of nowhere, that she'd think the two she was stalking had done it somehow...lol. I'm able to freerange, so when outside the run, I'd chase her if she acted that way (like you, I kind of felt bad about that part).
Other than that, the only thing I can think of is wiring off a section of the run for just her (or her and a buddy), and putting a covered litter box or somthing in there for egg laying. Then let them roost with the others at night, but back into their own area the next day????