When you say FD is sometimes grown on a medium other than skim milk, do you mean another dairy medium, for example whey? I understand that great care is taken to eliminate pathogens from commercial cultures in general and that they are highly pure. They are sure to be safer than many other food products. My concern is due to the nature of prions--if present, they would be inside the cultured microbes, as they would be inside the cells of a food. If you eat non-organic animal products, commercial cultures do not increase your risk of disease. It's difficult to know for sure, but that may not be the case if you only eat organic animal products or no animal products.
Since organic cow feed is not allowed to contain any animal products, not even chicken fat or bone meal, and the animals have to be born on an organic ranch, I do feel the risk of prion transmission from organic dairy is as low as for vegetables (only contamination would come from contaminated manure fertilizer on fields). Unfortunately prions survive any amount of heat that food survives, so autoclaving is not an effective prophylaxis. By the time the symptoms of prion disease are evident in a person, it's almost impossible to determine what it was they ate years before that caused it. It could even be from their mother's breast milk--indeterminable if she died from another cause before showing symptoms.
I may be whistling in the dark, but I'm going to call some small organic dairy producers in my general area, and see if they can help me.