I believe the $250K was for contempt of court. Not for humanely raising and selling food to willing customers. (Is the willing redundant there?)

It seems that in late 2015, the Food and Drug Administration, isolated and identified Listeria monocytogenes (L. mono) bacteria in samples of Miller’s raw milk; through whole genome sequencing, found the bacteria to be genetically similar to L. mono in two individuals who had developed listeriosis (with one dying) after consuming raw milk; and named Miller’s as the “likely source” of those infections.

So they went to the FDA to get access to the farm to inspect the operations. They haven't gotten the ordered access over the past 5 years, and now the Judge reckons it's time for them to do something about the repeated orders to allow inspections not having any affect. Hence the $250K.

To be fair, he could allow the fucking inspections.