In my honest opinion, PetCo is a terrible place for reptiles to be... They take alright care of their dogs, cats and ferrets and whatnot, but they just don't know how to take care of their reptile creatures. Namely: Chameleons.
The best case scenario is you tell them that you've noticed she's got MBD and they're all over it and know what to do to help her. But that's most likely not the case.
You should definitely mention to them you noticed that and that you'd like to see her being correctly taken care of. Hopefully they'll be open to your advice and whatnot and will handle the situation accordingly.
If you could take her in, that'd be the best for her... I don't know that I could legitimately state that she's going to make it in their care...
It's extremely sad, but true. I was in PetCo just a couple weeks ago and the person told me that most of their chameleons die because they're "just too small," "aren't strong enough to survive," and "actually, most chameleons die when they're young in the wild
and captivity anyway, so it's sort of a guessing game." All just sad lies...
I really hope for the best for the little girl!

Good luck!