That's a really tough one.
I would actually get in touch with a lawyer, if you can at all afford it. I was bullied for years in school, my parents constantly talking to my teacher and the headmaster about how to stop it but nothing really ever happening. Usually, it wasn't all that bad. I had my glasses broken and was constantly taunted, and sometimes chased, but then, one day, a boy in my class threw a sharp knife into the wall right next to me during woodworking class...
My parents decided enough was enough and contacted a lawyer and threatened all involved (including the school, since they had legal responsibility for my protection during my travel from home and to school) and suddenly from one day to the next, things stopped. Just stopped.
It was a very strange experience. Years and years of bullying...just stopped, because of a law-suit threat. We didn't even have to follow through with it. The fact we suddenly had economically potentially very sharp teeth made all the world of difference.
What I would do right now, if possible, is to give your daughter a day or two at home. Call the school and tell them why. She probably needs it, just to be able to collect herself and calm down a little. I know, I know...it is frequently said that you should never let a child be at home after being bullied because then they will know that is an option and develop tummy aches and whatnot. Seriously though, this is more than just being bullied. No child should have to face being thrown rocks at!
Then, I would look into the law. Especially what responsibilities the school has with regards to keeping your child safe while in transit and during school hours. It might perhaps be arranged that your children is picked up separately from the rest (like special needs kids can be, at least here in Sweden) or at least that there's a friendly adult person at the bus stop to ensure that the worst girl is not at the stop and to be able to identify the rock-throwing kids so that the police and social services can be contacted. The act of stone throwing is, after all, actually an act of physical abuse. Since the kids are so young, their parents are really responsible for seeing to it that they do not do illegal things. Failing to do so, and it really does become a case of parent neglect and thus social services should step in.
One thing I do wish my parents had done is to actually move me to another school. Give me a chance for a clean slate...they never did, of some reason. Perhaps because they figured that with my glasses, my stuttering and my penchant for classical music I would soon be bullied again (I have very realistic parents). But since your daughter is seemingly bullied because of an act of very malicious misinformation (by the way...is that not a crime? Spreading false rumours about a person which can harm that person?) it might help to look into moving her and your son to another school. It doesn't mean they will loose the friends they have, but it might mean a new chance. Even if there are kids knowing the kids whom bully your daughter at that school, they might not be in a strong position in another school.
p.s. For the run-on the-mill bully my father taught me some self-defence. In the case of your daughter, it is not really advisable because of the risk of there being knives involved...but when things calm down a bit, it might help her self confidence and make her feel safer.