The point of the article wasn't actually about smoking. At least that's not what I took from it.
I also don't think the author is genuinely claiming there's a conspiracy here.
Instead, what I took from it, is that being a scientist does not mean you're immune to prejudicial opinion, and that the scientific community is not immune to its own dogmas.
In theory, the scientific method should resolve that. But in practice, scientists (including the medical community) are just as apt as anyone to want to confirm their biases and dismiss difficult evidence.
I also think when it comes to anything involving public policy, things can quickly devolve to no longer being about scientific inquiry but rather about supporting or attacking positions.
Maybe I'm wrong. Maybe the author just wants everyone to start smoking and stop listening to their doctors. But that's not how it came across to me.
I think it's more a call for critical thinking and fairness. Just because an issue has been politicized, doesn't mean we should pick a side.
For what it's worth, I'm opposed to smoking and and supportive of vaccines. But if the day comes where there is strong evidence to suggest switching positions on that, I'd like to think I'll be open minded enough to do so.
Final point, briefly touched on in the article: Nicotine deserves more research. Almost all research on nicotine is in terms of smoking tobacco. Nicotine on its own could very well prove to be an important medical drug.
Same for all drugs... THC, CBD, whatever the active substance in cocaine and heroin are. They should all be studies rigorously and without moral judgment.