The thing is, she has an ace in the hole if there is a confrontation with BB. The Nu-humans. Most of them have never met BB, and they certainly have no allegiance to him. He hasn't been around for them at all. Medusa, on the other hand, has personally sought them out, offered them shelter/protection, and been there for them from the beginning. I could very well see them siding with her if a conflict arises.