If there are already subsidies why can’t there be subsidies specifically for adopting organic methods. You could also make the subsidies pay more during the first few years of the transition period.

Milk is very subsidized as well. You could pair local dairies with local farmers participating in similar programs.

That's the million dollar question. There are reasons to subsidize overproduction of food and plant-based biofuels (ethanol) -- food riots are bad. So the current system makes sense even if I don't agree with it 100%. I anticipate we will see governments study/adapt these subsidy markets for more eco-friendly practices (for the purpose of carbon sequestration and/or ground water protection).

Each farm is different - in fact within a field there is enough variation that the best management is not the same across the whole. Thus you cannot subsidies any one practice.

What the subsidies do is subsidize insurance. Buy insurance and if you have a crop failure you get paid as if you had the average yield over the past 10 years. However your average goes down as well for the next failure so better not have too many bad years in a row.

Organic despite the name is not the best thing for the environment. Some of it is, that quickly is normal farming. What is left is not using safe chemicals, instead using much more harmful - but natural - ones, or tillage to control weeds. (Note that this article is pushing no-till which is conventional farming today)

The incentive structure for the people involved in asking for and deciding upon the subsidy structure is heavily weighted in favor of getting the subsidies at least cost to the business. Effectively, large ag producers are faced with a choice between "getting subsidies for labor-intensive sustainable practices" and "getting subsidies for machine-intensive practices".