Not long ago I made one of my periodic forays to Whole Foods, the all-natural-groceries conglomerate. My assignment was to buy a Christmas ham from a pig that had not suffered unduly, and that was relatively free of chemicals and antibiotics.

I was somewhere between the Amy's organic soups and the own-label cans of vegetables when I came upon an unexpected sight: bottles of Heinz regular ketchup that, like much of the industrial food that comprises the American diet, is sweetened with high-fructose corn syrup (HFCS).

As you may know, HFCS is among the laboratory-created synthetic foods targeted for elimination by activists, most notably the journalist Michael Pollan in his influential book The Omnivore's Dilemma. Though scientific opinion differs on whether HFCS is any worse for you than regular sugar, there's little doubt that its cheap ubiquity – a consequence of misguided government farming subsidies – has contributed significantly to our epidemics of obesity and type-two diabetes.

Thus I considered it a breach of faith that Whole Foods would carry such a product. Shopping there means you're going to pay more and drive farther than if you simply stocked up at the nearest supermarket. In return, it doesn't seem too much to ask that you be spared from having to worry about ingredients such as HFCS. So it was with a perverse sense of anticipation that I started reading Nick Paumgarten's 9,100-word profile of Whole Foods founder and chief executive John Mackey in the current issue of the New Yorker.

As Paumgarten observes, Mackey has stepped in it several times in recent years, engaging in embarrassing (and legally dubious) internet sock puppetry with regard to his acquisition of Wild Oats, a rival chain, and writing a commentary for the Wall Street Journal in opposition to government healthcare reform. The latter enraged his largely liberal customer base, engendering brief calls for a boycott.

What makes the New Yorker article valuable, though, is the way Paumgarten captures Mackey's "crazy uncle" and "right-wing hippie" personae and places them in the context of his radical libertarianism. In the course of talking (and talking, and talking), Mackey reveals an important contradiction that illustrates why Whole Foods simply isn't as good as it should be. On the one hand, Mackey, now a vegan, is absolutely committed to healthy food. On the other, his naive belief in individual responsibility informs not just his contempt for government but, in a sense, for his own company as well.

Consider, for instance, Mackey's much-criticized statement that "We sell a bunch of junk." In fact, Whole Foods sells meat, which Mackey eschews, as well as nutritionally empty snacks. This is not necessarily a bad thing. Meat, candy and potato chips have been with us for a long time, and, in their unadulterated, pre-industrial incarnations, were considerably less toxic than they are today.

But Mackey's libertarianism means that the consumer must always beware, even at Whole Foods. As Paumgarten writes of Mackey:

His belief in the power of the individual is such that blame falls on individuals, too. In his view, it tends to be the fault of the unhealthy or fat person that he or she is unhealthy or fat. People just need to eat better.... It matters less to him that our food system, for a dozen reasons, ... has been rigged to deliver unhealthy food at artificially low cost to a misguided public. People have the power and the means to choose rice and beans over Big Macs, and when they fail to do so they bring ruin on themselves, and on everyone else.

The trouble with this type of thinking is that, at its end point, it's our own fault if we buy ketchup loaded with high-fructose corn syrup – even if we got it at Whole Foods. After all, there was a shelf full of Heinz organic ketchup next to the regular variety. If you choose the cheap stuff, what concern is it of Mackey's? Whole Foods is a store that sells "a bunch of junk", not a shrine.

Except that Mackey misconceives an important part of his business. At a time when even Walmart is carrying organic foods, the niche Whole Foods ought to fill is that of the trusted guide. If I have to walk the aisles of Whole Foods with the same label-reading skepticism that I bring to supermarket shopping, well, I might as well go to the local supermarket. It carries more natural and organic foods than it used to, it's closer to our house and it's a lot cheaper.

Besides, as Paumgarten writes, Mackey's libertarianism ignores larger social and cultural forces. My wife and I would love to do better than Whole Foods – to buy most of our food from local farmers, and to leave the industrial-food system altogether. We've tried. But unless we are willing and able to devote a lot more time and money to the enterprise, the best we can manage is to buy produce from farmers markets during the growing season and milk from a nearby dairy.

For us, a place like Whole Foods should be an important way station between industrial food and something better. Mackey seems to understand that, but his blind exaltation of the individual misses some pretty important caveats.

Individuals live in a social setting, turning over some tasks so that they can specialise in others. I don't want to perform my own surgery or maintain my own roads. And I don't want to come home from the grocery store with unhealthy food only to be told it's my own damn fault.

Especially if I bought it at Whole Foods.