I think this type of bullying or social castigation is especially common in female circles. It's interesting that you posted this because one of our local morning radio programs spent a large portion of the show a couple of weeks ago discussing bullying, the new movie Bully that's just come out, and they had some bullying experts on the show who pointed out some very important points about bullying.
First and foremost, they stressed the difference between bullying and conflict. Both situations obviously make you uncomfortable, but bullying only occurs when there is an obvious imbalance of power or strength and one child has difficulty defending him or herself. Conflict, however, involves antagonism between two or more people, and it sort of sounds like what you have here is more conflict than bullying. However, from my experience, in female groups bullying and conflict sort of go hand-in-hand (in other words, both groups are involved in spreading rumors and calling names which is bullying).
Now, there can be a slippery slope from conflict into bullying, especially if your daughter is concerned that if she spends time with both groups of girls that she will ultimately be ostracized by both groups--and social isolation is a common form of bullying. Is she receiving negative feedback from either group because she's trying to hang out with both groups? If not, then I think you're doing the right thing by encouraging her to be friends with girls of different groups and helping her manage her anxiety about that.
However, if her friends are starting to turn on her because she's trying to be friends with girls from other groups, then that is something that needs to be addressed differently. I don't have a great answer, but I can recommend what the local radio show told its listeners (and I know this will work for you since you're here in the United States). They recommended that you contact your area Anti-Defamation League who has gotten really involved with its anti-bullying campaign and has a lot of stuff on its website about bullying. If you can't find the answers on their website, you can contact them directly and speak to someone about your situation and they might be able to tell you how to handle the situation better.