The reply has some legitimate criticisms of the original article (it doesn't say anything about pesticides, and newer studies may indeed change the outcome (and you should always take these sorts of meta-analysis with a grain of salt)), but it doesn't seem to contradict the basic claim of the original article that nutritionally organic and conventional food are about the same other than by citing a different meta-analysis by The Organic Center (no bias there :) that had a forward written by Dr. Andrew Weil, a know quack. Now The Organic Center's report may be correct, I'd have to read both analysis, and probably all of the studies in both of the reports to figure out which is more trustworthy, but I certainly haven't seen anything that can dismiss the study in the original article out of hand.
There were a couple of other things that troubled me about the reply, most obvious of which was the conflation of organic and sustainable food. Organic only means that certain pesticides, fertilizers and (in animals) antibiotics are not used. There is no evidence, that I am aware of at least, that organic food is significantly more sustainable. It may be somewhat better, it may be somewhat worse (certainly if you are shipping it all over the world it isn't sustainable in the least, not that conventional food is any better in this count), but organic does not imply sustainable.
I agree with the goals of the organic food movement, and I often prefer it (when I can afford it), because it just tastes better. I'm not deceiving myself that organic food is a cure for America's problems with agriculture though.
For those of us who are not part of the Vegan/Vegetarian groups there may be a difference when it comes to meat and dairy the U.S. and Canada (as far as I'm aware this is still the case) because of the use rbGH/rBST. The problem I've had is that due to the on-going and heated trade issue this has brought about with the E.U. (they have been blocking meat from both countries) it is very difficult to find unbiased or even minimally biased information on the subject. There is also a great deal of money to be made by drug companies and the reduction of cost by making greater quantities of food.
It is all good and fine to say this should not be done, but we also need to find a way to make sure that the population can be fed safely and effectively. It is a hard call and a big problem. Like everything else, it is all interconnected; not in a conspiracy type of way, but in a the world is really not as big as it seems sort of way. For now we are sticking with regular fruits and veggies, growing what we can and buying natural or organic meat and diary. I have enough of my own hormone issues, it is not as if adding some from animals will help me.