At any rate, this blog post provides the quote in question, from page 229 of "Omnivore's Dilemma" though it turns out it's the USDA, not the FDA that is mentioned.

http://www.businessweek.com/smallbiz/running_small_business/...

Here's the quote: "The problem with current food-safety regulations, in [small farmer Joel Salatin’s view], is that they are one-size-fits-all rules designed to regulate giant slaughterhouses that are mindlessly applied to small farmers in such a way that “before I can sell my neighbor a T-bone steak I’ve got to wrap it up in a million dollars’ worth of quintuple-permitted processing plant.” For example, federal rules stipulate that every processing facility have a bathroom for the exclusive use of the USDA inspector. Such regulations favor the biggest industrial meatpackers, who can spread the costs of compliance over the millions of animals they process every year, at the expense of artisanal enterprises like Polyface [Salatin’s farm]."