What are ways to compare the "costs" and "gains" of food production systems?
Calories and dollars are the most obvious and straightforward, but including additional variables complicates the accounting. . A great paper that used energy has been updated in a more recent publication. Emergy is an interesting alternative. 

Current work includes the Natural Captial project that "aims to integrate the values of nature into all major decisions affecting the environment and human well-being". Of course, this approach exchanges a simple currency for a more comprehensive one. 

Climate regulating value is also a relatively straightforward and relevant currency that can be used to compare the value of food production systems.