First of all, even if your sister doesn't have strep, she could theoretically have a bacterial infection. I had pharyngitis once in college that the Health Center insisted was the flu and refused to give me antibiotics for even though it persisted for over a month. Finally, VERY SICK, at the beginning of summer, I went home, was diagnosed, given antibiotics, and cleared up. I still think I would've done better with finals and moving (this was my freshman year, and the end of it was hell because I was perpetually sick without proper care) and not been miserable for over a month if someone had listened to me when I knew it was not the flu. Nothing in your post suggests anyone is 100% sure your sister has the flu. (The campus health center did a strep test on me back then by the by, and it was negative - because I didn't have strep - but strep is not the only bacterial infection.) My point is that while calling in antibiotics for a patient you haven't personally seen seems a bit irresponsible to me, this notion that she has "strep or flu" is equally ignorant and doctors (especially at emergency walk-in type places or campus health centers) often go too far in their worries about creating resistance and not prescribing antibiotics. Realistically, there is sometimes no way to "know" whether someone needs antibiotics or not until they've been in pain for a long time. While a viral infection doesn't "turn" bacterial, bacterial infections can certainly 'piggyback' and occur after a viral infection has weakened your system. The flu itself can also have bacterial complications, though your young, healthy sister is probably not at great risk for those.

Second of all, I think you're being a little intense about this. Yes, the overuse of antibiotics contributes to creating more resistant bacteria...but like to a fairly small degree in circumstances like this. There are other contributing factors. If a super bacteria emerges, it will probably not be because your sister took antibiotics for something that might've been the flu, might've been something else.

I really think your sister should've just seen the family doctor to begin with. An emergency care clinic is going to learn TOO much against prescribing antibiotics when they may help (they will often require 100% proof of a bacterial infection, which is not always doable) whereas a family doctor is more likely to balance that medical reality with the patient's comfort in the fact of various possible causes. It's really almost impossible to KNOW what is causing your sister's illness.