That's a concern for vegans, though frankly, there's really no such thing as a vegan--just people who like to pretend they aren't using animal products. That said, there are occasionally (not always) nutritive merits to organic food--not so much when it comes to plants, but specifically with meats. Factory farmed animals/eggs/milk are lower in omega-3 fatty acids because their diets are formulated for cost rather than nutrition--whereas free range animals have a much more balanced diet.
Of course we could easily fix this by throwing some flax seeds in with the corn and soy. We don't really have to get rid of modern farming techniques to get healthier food, just revise them a bit and perhaps spend a tad more on feed. But, that's only going to happen if their is consumer demand for it and many of the people who feel strongly have essentially "opted-out" of the voting process by becoming vegans/vegetarians. We could address a lot of the complaints vegans have about how we treat animals in this country by simply having an "ethical meat eating" movement to replace veganism.