...or species out-evolving out food crops and overtaking them. With far more fuel the odds would be in favor of species that can consume nitrogen, and how do you keep those at bay when it happens?

We have always had this problem of other species outcompeting crops - we call the undesired-but-superiror-plants "weeds" and traditionally they were removed mechanically. The 20th century saw the invention of achieving the dame task via sprayed chemicals such as Round-Up.