My theory if she's the Rani is that she's working with people who do think that little Melody is a weapon against the Doctor, but her true plan is to use Melody as the type for a new generation of Time Lords. I think that the people she's working with don't know she's a Time Lord herself, or if they were able to check that she somehow managed to turn herself biologically human while retaining all of her identity and memories. Unless she's managed to do the Zaphod Beeblebrox thing and turn herself into an amnesiac human with subliminal drives to fulfil her original plan.