I suggest that you provide her with lots of leggings to wear under her short skirts.  Leggings are very trendy now, and wearing a short skirt over them gives the look that is "in" right now, but the body is better covered.  I've seen this look from some young teens I know, and it allows them to remain stylish, while maintaining a certain level of modesty.  I think your bottom line is that she should dress according to her school's dress code, unless you are intent on doing what you're doing.  Good luck with this precious girl, who so wants to fit in, but hasn't really yet found her "look."