Fluoroquinolones are drugs of choice for a variety of severe infections, so I doubt they'll be going anywhere any time soon. There are risks with nearly all treatments. You have to weigh the potential for side effects with the potential consequences of NOT treating.
Certainly. In many cases, you have no choice - take the drugs or die. However, there are a few issues with that.
1) Few doctor's know the risks of the medications they prescribe because health education sucks, even at doctorate-level. The reason for this is simple - the state wants money, and they regulate the organizations that manage healthcare in this country. Their goal isn't actually "cure" the individual, it's to make money, and as a prerequisite to that, treat patients. They are not concerned with the individual, they are concerned with statistics. That 99% success rate on Cipro seems great, until you're the 1%.
Since things are calculated based on statistics, the doctor's don't actually need to know what the medications they prescribe do (according to the state), they just need to know what to prescribe for what symptoms, and "treat" as many patients as they possibly can - they literally have a quota that is ultimately determined by the state.
So, if a doctor doesn't know what these prescriptions do, how can the patient? "Informed medical consent" my ass =\
2) For some time, leeches were a "drug" of choice to deal with illness, as was exorcising demons. Did it help some people? Probably - at least, they thought it did. Was it the "best" choice? Definitely not. Drugs like Cipro can be viewed the same way... Particularly considering reason 1 above. Just because Cipro works, doesn't mean it's the "only" drug.
3) Worth noting... No gamble is worth your life. Unfortunately, considering 1 and 2, people aren't usually aware of what they're gambling for or with. Why? Because the state refuses to allow proper research and distribution of information on medicine - all they care about is money, and thus statistics. Even if 49% of people died on a drug, and 51% survived, if they could cover up the fact that the 49% died to said drug, they'd probably let it pass because it is "statistically successful." Hell, some extreme operations have worse than a 50% success rate, and they're legal.
Also, I've been to two major hospitals - John's Hopkins and Mayo - for my own medical issues. John's Hopkins had some success, but failed in the later stages. Mayo was a joke. My point is this - your professor may be an expert at a major hospital, but that doesn't mean anything in regard to reliability of information. Frankly, other than empirical evidence, no evidence is reliable. It's far too easy to misrepresent, manipulate, and even forge information.