Yes, if you suddenly confront some strange physician and demand a prescription for Flagyl, it is likely that he will refuse. On the other hand, if you ask your regular physician, and if you support your request with some medical literature references or statistics and explain the situation, you will stand a better chance. Also, it is possible that the physician will want to prescribe some other drug that is not as powerful.
My personal physician knows that I am not a "druggie" and he knows that I am not a complete fool about this stuff. If he doesn't know which way to decide, he refers me to the Travel Clinic of the same health center, because they have more experience on this subject.
Yes, my standard protocol when in a third-world country is much deeper than when I am out along the PCT. If I feel the first urge of a serious GI problem, I take Pepto-Bismol tablets, maybe one or two. If the urge becomes more demanding, then I take Immodium. If that doesn't clear it, then I break out the Bactrim or Cipro. Note that each drug has its own minor side effects.
It's more likely along the PCT that a mild case of something is triggered by poor cleanliness with your eating gear. It wouldn't shock me a bit to hear of somebody getting "full blown" Giardia [pun intended].
What would be really neat to know... is there something slightly different in your GI tract, and that explains why you got Giardia when the next hiker didn't. I can understand if you had failures in your water treatment system. But, wouldn't it be interesting if it was determined that you had something that could have been detected by a lab test? Like, you had been eating Food Item X, and that is better for Giardia bugs to survive. That's just a wild theory. The Giardia cyst is a tough little thing.