go with either fixed gear or single speed, though i'd recommend the fixie (no need for a rear brake, then, to get in the way of an out of true wheel --happens a lot on these streets). just get her used to riding one before she moves.
yes on the armadillos, but lose the toughies. no need to weigh down the wheels that much.
try to get her to wear a helmet. they suck, but they work. it's not a matter of "if" but "when."
if you opt for a flat bar (not recommended), chop it down to avoid those annoying side mirrors that cars sport. also, use bar ends, but rotate them to lateral to protect her fingers.
i recommend getting Kryptonite locking skewers for the wheels. they run around $55. take an old chain and run it through the saddle bars and around one of the seat stays. this will keep the saddle as safe as possible.
like the other post said --NO QUICK RELEASES. even if you don't take the advice above about the skewers, don't have any quick releases anywhere.
also, get a New York Chain from the Krypt. even when the bike is indoors, she should lock it to something fixed to the building. never lock up outdoor overnight. things will be missing in the morning.
oh yeah, she should attend the critical mass at union square. last friday of every month. what a party.