I think a few things should be kept in mind:

The nutritional quality of any foods is affected by the soil in which its grown, the breed of the particular crop and the time between harvest and consumption. Grow two types of tomatoes in different fields, then test one at harvest and another a day later and the differences in nutrient quality will be dramatic. And not all the studies cited controlled for these variables.

But the biggest drawback in the study was what it failed to consider: the impact of pesticides used in conventional agriculture, which has been the most significant reason that people have chosen organic food, especially for children. As the study stated:

All natural products vary in their composition of nutrients and other nutritional relevant substances for a wide variety of reasons, including production method. Production methods, especially those that regulate the use of chemical fertilizer, herbicides, and pesticides may also affect the chemical content of foodstuffs. Certified organic regimens specify the production of foodstuffs with the strictly controlled use of chemicals and medicines. The potential for any benefits to public and environmental health of these actions would certainly warrant further systematic review, but was beyond the scope of the current report.

Studies have consistently shown that organic foods have less pesticide residues than conventionally grown foods. Do those levels make a difference? That depends on the degree and length of exposure and the health and age of the subject. While it is known that chemicals have the most dramatic impact on fast-developing organisms (infants and children) the effects potentially develop over decades. 

While conventional producers have, in some cases, reduced chemical pesticide use in favor of more measured applications, other indirect effects are still prominent -- fertilizers poisoning drinking water sources being a prominent one in the Midwest. 

In short, the study will hardly be the last word on this issue. 

- Samuel Fromartz