That food should be fresh and natural has become an article of faith. It comes as something of a shock to realize that this is a latter-day creed. For our ancestors, natural was something quite nasty. Natural often tasted bad.
There are some good points here, although the article needs less pretentiousness and more citations, IMO (for "an historian", the author provides surprisingly few sources for his claims). I think that the argument against equating "freshness" with "healthiness" is not a bad one. Fresh food doesn't always mean safer to eat or healthier. However, I think the article downplays the issues of pesticide use, GMOs, battery farming, and so on, instead going on a lengthy ramble about how unhealthy "fresh" food can be. I think that the real answer lies somewhere between the author's point of view and those of the "food luddites" he describes -- having a mixture of "fresh", in-season food and processed, out-of season foods. I expect that this is actually how most "food luddites" actually eat already.
The "ethos" proffered at the end of the article is not a bad one, but it seems too vague an answer for a complex problem. The issue of deciding "case by case when natural is preferable to processed" is interesting, but what criteria should be used for this? Is it possible for individuals to make such decisions given how far removed most people are from the food they eat?