Farming is a technology that humans developed (over thousands of years) to get more food, bred to serve the whims of humans, with the least amount of effort. That was what farming was 5,000 years ago. That is what farming is today... although today we have gotten better at it.
The things that make modern farming efficient (such as fertilizer and mechanization) are just extensions of the technology of the past. The idea that farming is "natural", given the fact that it has been a technology since the beginning of time, is not rational.
Of course farming is effected and reliant on "natural processes". But so is mining, and oil drilling and construction and many other human endeavours. Farming is simply a collection of technological advancements designed to produce food.
Policy, whether global or national or local should be based on facts rather than ideology. It is reasonable to raise real concerns about modern agriculture, such as that fertilizer is running off and hurting estuaries. That way we can have a discussion, look at facts and possible solutions, and come up with a reasonable response. It is not reasonble to based policy on mythology; such as the claim that conventional farming methods lead to food with lower nutritional value. Valid claims can be tested and supported by fact.
But the real issue is the ideological bias that says that some foods, or farming methods are "natural" and others aren't natural. Once you do this, you aren't basing policy decisions on facts and evidence, it is all about ideology.