The author seems to be saying that rigorous, peer-reviewed, observational studies should be the end of the discussion, or at least the starting point. I'm not sure I agree. Given the significant limitations present in all medical studies like this, I think it could make some sense to give a lot more weight to the conclusion reached through a fundamental understanding of how the human body works. Some hesitancy to overturn that conclusion based on a handful of inevitably flawed studies seems prudent to me, or at least not crazy.
I'm reminded of the current tensions around "evidence-based practice" where medicine is transformed into essentially flowcharts that get continuously updated according to peer-reviewed research. It sounds like a good idea, but it's been somewhat controversial since that's not how medicine has traditionally been practiced. It significantly reduces a doctor's ability to problem solve through reasoning, which has some benefits but also some clear downsides as well.