Other than her height (which isn't THAT short), there's no difference between a new female rider and a new male rider. So consider any and all "starter" bikes that one would recommend to any other new rider. The Ninja 250, the Ninja 500, the GS500 (which has a sportier look than the smaller Ninjas), the SV650 and SV650S, and the Ninja 650.
Also, consider an older 600 series bike (an older ZX6R or an F2 or F3 can make a great starter bike for more mature riders... it's still a 600, and therefore powerful, but not a fraction as fast as NEW 600cc bikes).
If her objection to the SV is the naked look, consider this: a full fairing kit can be added for about $1000, and totally changes the look. They look excellent full faired (but at the same time, I'd urge her NOT to install fairings until she's got some seat time under her belt -- as we all know, she WILL drop the bike at least once in the early months, so it's better to just scrape up a frame slider than pretty new $1000 plastics).
As for "outgrowing" a 500cc bike too soon... I've known plenty of people who ride and stick with a 500cc bike long past "beginner" status. 500cc is still a respectable bike. Also, 250's and 500's can often be ridden for a year and turned around and sold for darn near what you paid for it, so you could always make her a deal like "Ride the snot outta this for a year, then we'll upgrade you once you've got some experience under your belt."
With regard to the not touching the ground, check this site for seat heights of many motorcycles:
More important than her height is her inseam, so keep that in mind when shopping.
As mentioned above, good riding boots can gain her some height as well. SIDI makes very high quality riding boots, and have some styles for women that can gain her as much as 2 inches.
Another option is to shave the seat -- I know of a girl who's barely 5'0" who got about 1.5" by shaving the foam in her seat (then once she was better acclimated to the bike, she replaced it with a stock seat for better cushioning).