Speaking as a vertically challenged person, a 46-48cm frame with 700c wheels presents a different problem: toe overlap.

I have a 43cm Indy Fab Crown Jewel w/700c wheels. I don't ever go fast around turns and pedal at the same time, it's that severe.

650c wheels are much better suited for shorter riders, but you're not going to find a 650c MTB frame. I suggest finding her a nice 650c road frame as an alternative.