Technically, Storm has been controlled by nanites before in canon. Personally, I don't think it makes any sense given the huge amounts of electrical energy she generates and channels. It should short circuit the nanites, but it doesn't. So, I never really complain about nanites working on Ororo as they seem to work on everyone. That said, her mind being altered should not affect her immunity as that is dependent on her bond with the universal life force around her.