Shelke is going to be pro-Initiative. They've taken care of her, they provide her with her medicine, and from her perspective, they saved her life. She won't directly fight the mutineers unless they get in her way, but she disagrees with them completely (and will hopefully be helping to restore the network).

Elizabeth is neutral...she doesn't particularly like the Initiative, but she has absolutely no faith in grass-roots freedom fighter anti-establishment types claiming they are doing what is best for everyone. She's seen what groups like that become (in worst case scenarios) and will never side with one again.