While I think the article/oped is rather lacking and is way too superficial, I have a few comments (as well as a few criticisms of your criticism).
1. I found the juxtaposition of Pomegranate and Purpose (gashmiut and ruchniyut) to be delicious, especially as he used the store as his intro into orthodox Judaism.
2. I don't believe there was anything nefarious (nor misinformed by his guide) in his writing "modern Orthodox" and "Chassidic". The fact is that the word Charedi didn't exist (or wasn't at all popular) 40 years ago, and New Yorkers of that time used Chassidic to cover all those Jews that either wear mostly black and white, or have sidelocks, or wear furry hats or fedoras. So Yeshivish/RW were lumped into "Chassidish" for many (including me). Today we use Charedi to cover both classes with Chassidish as a sub-group within Charedi (or Ultra-Orthodox in the USA).
3. I have a different problem with him writing "modern Orthodox" in relation to that store. I've only been to the store 3 times in my life, each time on a Friday, and each time the store was PACKED. However, the vast majority (pretty much everyone except for me and the other MO fellow I was with) of the people shopping in the store were clearly Charedi (or what he would term "Chassidic").
4. I dislike his use of the word "counterculture" in this context, Usually counterculture is used to mean a reaction against prevailing society. Orthodox Jewry is not a reaction against society, but rather a striving to live as a different society. People rarely become orthodox as a "rebellion" against prevailing society, usually they are drawn in by various aspects of it. I think it's the wrong word to describe the phenomenon. Would he describe Amish as reacting against prevailing society - no way.
5. Dairy-free (and gluten-free) items are not unique to kosher markets, nor are pre-cut tableclothes. In fact, those things are commonplace in every market in the USA. They have nothing at all to do with orthodox Judaism. Very few people cut their own tablecloths at home (almost every institution, including my shul, does, but that's because they have tens of tables to be covered for every event). Every party goods and supermarket around the country sells pre-cut tableclothes of varying sizes. In fact, I have rarely seen the large rolls of "cut your own". And regular stores carry a wide variety of sponges (including those silly net kinds that don't hold water).
6. If he really wanted to note something religiously unique to the store, he should have noted the annual Purim and Chanukah decorations (as opposed to the usual Halloween and Christmas decorations in most markets).
7. "their shopping is minutely governed by an external moral order." This is a ridiculous statement. What we do and eat is minutely governed, and even what we shop for in non-kosher stores is governed, but this store is just the opposite! Because everything is kosher, we can walk in there and buy anything we please. In fact, that's the entire reason the store exists in the first place.
8) The metaphor. So many yeshivish metaphors are silly, this is just another one to add to the list.
9) Much of the delight. Oy vey! Someone needs to invite him to a tish - no learning or arguing over arcane facts going on there, just fressing and fighting over the closer spots to the Rebbe (to catch food that he touched). Or to a kiddush club, no expounding over ancient texts, just drinking good adult beverages and having fun conversation with friends. Or perhaps a shmorg at a Jewish wedding. Or the dancing at a Jewish wedding. Or the hundreds of other things we do for "delight". I dislike the stereotype of the Jew only receiving delight while hunched over an ancient tome or arguing over arcane facts. Sure we (some of us or even many of us) receive delight from those things, but not solely those from things.
10) Inaccuracy. The wife of the Rabbi didn't go to a "Yeshiva". If anything she went to a seminary or to a women's college.
11) Possible new fact (depending on how good his research was). Only 71% of orthodox are married by age 30. This means that the shidduch crisis is larger previously described (at 10-15%). I really would like to know where this number came from. Is it true that almost 3 out of 10 orthodox 30 year-olds are unmarried? Somehow it doesn't seem that way.
12) Finally, Pomegranate struck me as quite expensive. Did Brooks even glance at the prices? I doubt the shoppers there represent a good cross section of orthodox NYC, certainly not the Chassidic parts. It appeared to me that the well-heeled orthodox Jews shop there, the less well off shop at other places in Flatbush or in Boro Park. Someone should take him to the Kollel store once. He might comment about "sticky worn-down floors" instead of "nicely toned wood flooring" :-)