I'm not sure if you are the group leader or just asking as a mom of your own daughter.
If you are the leader, I would have a parent meeting with all of the parents without the girls present to discuss this and have everyone help brainstorm what should be done. If this is truley an organization that teaches self-esteem building activities, all of the girls need to find a way to stop excluding these 2 girls. You say you want some of that to seep through-- so the other girls need to stop bashing these 2 girls self esteem by excluding them. If they truely are bi-sexual, they will have enough people in their lives treating them poorly based on their sexuality, so if they are in a group with girls who are supposed to be a sisterhood, they ought to be able to feel comfortable around the other girls and vice versa-- So the parents need to brainstorm ways to talk to the group of girls about all of this and find even ground to make sure EVERYONE is comfortable.
You say these girls aren't homophobic, but I disagree. They aren't homophobic is a way that they HATE homosexuality, but they are PHOBIC in that they have a fear of the unknown. This usually comes from ignorance. For example, just because these 2 girls may be ATTRACTED to other girls does not mean that they will do anything inappropriate to any of the other girls in the group, and that needs to be discussed so that fear of the unknown can go away. If you are not the leader, suggest a parent meeting and see if the leader is open to the idea.
As a mom, you need to figure out what your own family values are and how you want to teach your daughter to treat others. If a girl did something harmful to my daughter or was mean to her, I could understand why she wouldn't want to be near that girl. But excluding someone because of their sexuality is not OK in my family-- any more than excluding due to race, religion, etc.