Hmm, I was going to say "Oh she should be fine, don't worry about it", but I feel differently after reading your second post. You're right, its a risk that is unnecessary, and a risk she'd be taking every single day for... 5 years? It seems likely that she'd eventually pick something up from the other girl. What was also alarming to me was the other mother's ignorance about CF in general. If your daughter had been that sick, wouldn't you have done a little research? I mean she didn't even know what bugs she was culturing.
Also keep in mind, you can catch things from hospitals and doctor's offices, and that is even with things being washed down, gloves, gowns, masks etc. Of course, there are MORE bugs going around in those places, but at a school you'd have 0 disinfection from class to class, maybe even day to day. What if they sit at the same desk in different periods? Same cafeteria table? Things like that I wonder about.
Like you said, your daughter is old enough to speak up for herself too. If she was worried and wasn't opposed to changing schools, it would certainly seem like a decent option. Years down the road if she had caught PA/MRSA from that girl and gotten extremely sick, you don't want to think "I could have prevented this."