This happened to me when I was almost the your age (I wonder if it's a college guy/high school girl thing...). Anyway, when I figured out she wasn't just flirting for flirts sake and it kind of fell on me (not literally, but close), to make a move or say um, thanks no. As it happened, I chose um, thanks no and I don't regret it (In fact, I had actually forgotten about the whole thing until I read this thread).
As far as how I did it, I basically told her she was really attractive and if I were closer to her age then I would have loved to, but that I just didn't think it made sense considering how far apart we were in age and in our lives (I mean, she was an intern and a junior in High School and I was about to graduate college. She acted so childlike I felt uncomfortable even being attracted to her). She didn't handle the rejection very well. She was very embarassed, didn't talk to me much after that, and quit the job not too long after. I felt somewhat responsible, but I didn't have any other choice as I saw it.
So, to answer your question, be honest with her, have the discussion and get it out of the way, and let her get over it however she needs to. I'm sure having a hot little girl dying to **** you is doing wonders for your ego, but if you're not going to have a relationship with her, you owe her that honesty so she can find someone else to throw herself at.