Something is going on with Molly, though. I think after that soul gaze with Thomas she was going to try to "help" him by mind bending him away from his demon, and THAT would not be a good thing at all. She could see it as just another adiction, and now that she "knows better" she can take care of it correctly. She also may have been nudging Harry in some sort of direction for some reason. She picked up quickly on what Pebody was up to with the nudging he was doing, and she was trying to read Luccio and Morgan's brains - such things could be considered Grey Magic.
If someone's shapeshifted in to Molly, the only person I can think of who Mouse would'nt raize the alarm on would be Mamma Margret. Mouse would know if Molly wasn't Molly, so if Molly isn't Molly, then Mouse has to be willing to protect whomever it is that is Molly. If Mouse thinks Margret is there to protect Harry as well, they may have made an agreement. That would make that scene with Thomas more about a mother trying to help her son who's in pain than a love struck teenager hit by a combination of vampire lust and soulgazing compassion.
She dosen't have to be Molly all the time, either. The real Molly could be dropping in for lessons and such and false Molly drops in at odd hours and just nudges Harry not to mention it when real Molly's around. Maybe that's a bit to complicated, but still possible. Here's the question... When is Molly's cooking good?