Anyone can throw in a silly comparison but it doesn't really help. I'm fairy certain you're smart enough to reflect on the nuance that this topic deserves. Some bad things are legal. Some bad things aren't. It's a complex thing for society to weigh up and the linked article attempts to contribute to that discussion.
I'm not being glib. This article is premised on the idea that because there are no health benefits to tobacco (none.), it has no value whatsoever. But it clearly does have value: it is a source of pleasure for a large number of people. Pleasure has value. People shouldn't smoke, it makes perfect sense to vice-tax it to offset the externalities, and nobody should valorize the companies profiting from those externalities. But the reason we "permit" it is because we have no business not permitting it: we have centuries of experience showing that, unlike opiates and methamphetamine, there is no risk of tobacco destabilizing society.
It's a comically weak argument. It could, as I just said, be applied just as readily to bacon.
Here you're picked the extremes to make your point stronger. There's plenty of prohibited substances and behaviours that are much closer to the gray area that this article is pondering on.
I don't have a clear view on this topic myself - but there's too many people in this thread claiming that it's absurd to even have the discussion - which I think is lazy and disingenuous.
Name a prohibited substance that (1) poses no threat of destabilizing society or the health care system, (2) has centuries of cultural context, and (3) isn't on the verge of being legalized right now, like cannabis and psilocybin.
The imminent legalization of psilocybin makes my argument for me. It was an argument isomorphic to the one this anti-smoking piece made that banned it in the first place. And as a society, we're charting a course in the opposite direction of that argument, because, it turns out, that argument was dumb.