Hydroxychloroquine seems like a weird example to bring up now, since it's been completely debunked.https://www.fda.gov/drugs/drug-safety-and-availability/fda-c...
Unfortunately, it means just "trusting a peer reviewed study" is even harder than it should be. You have to dig into the study to see if it even makes any sense which can be very difficult. And you have to follow the money, not "even" if the study says what you think it ought to say, but especially when it says what you want it to say.
Very disappointing when you go digging in.
Take for example acetaminophen (aka paracetamol/tylenol): it is borderline ineffective, has been superseded by ibuprofen for almost all use cases, and the required dosage for its tiny effect is also very close to dangerous levels. Yet it is still the go-to drug of parents, GPs and hospitals for a range of ailments from the common cold to post-operative pain. "Good old paracetamol" is in every medicine cabinet in the Western world. I've told my folks a hundred times that it simply doesn't work, but they use it for pretty much any condition. Mum even gave it to her old dog. It's trusted like oxo cubes, Campbell's soup or a nice cup of tea. And that's why it's the foremost cause of acute liver failure in the Western world. While it hasn't had it's approval removed yet, I wouldn't be surprised if it did some day, and I doubt it would be approved today if it were being introduced.
Even so: is it still very much "medicine", not "alternative medicine".
This is only really accurate in a small window of analysis. It's been shown that paracetamol + ibuprofen has synergistic effects for most pain-related issues and paracetamol is superior to ibuprofen for migraine headaches; furthermore, the obvious correct headache drug of choice is aspirin/paracetamol/caffeine, aka Excedrin, which is vastly superior to ibuprofen.
I won't argue that paracetamol has acute liver toxicity issues (the largest drug of overdose problems, though a lot of this is intentional rather than accidental), but ibuprofen is abused in a chronic fashion with buildup over time leading to renal failure and worse (pro/amateur athletes are particularly at risk of chronic abuse issues).
I won't argue that paracetamol is way more dangerous than people think, and there should be far more warning labels (which J&J fights against), but I would be genuinely shocked if it got its approval revoked; similarly, I'd expect it to be approved if it was around today as well - especially if we knew about the synergistic effects it has with aspirin and caffeine.