I don't feed in the cage and I practice rabid sterilization so I'm not overly worried about "cross-fecal contamination". I think that basic husbandry skills should eliminate that concern.
Don't get me wrong. I'm not advocating sacrificing the health of the snake for a larger profit margin, just trying to apply some common sense. When you feed more than 30-40 snakes at a single setting, you notice that up to 10-20% may not eat for various reasons (Shed cycle, breeding activities, ect) I plan for this and feed the ones that I think may refuse food first. If I am right and they don't eat, I simply offer it to another right away. For folks that earn a living breeding reptiles, tossing every morsal would be a substantial annual expense. I can't imagine that throwing out perfectly good food items would be a viable business decision.
I would be interested in hearing what some of the larger breeders have to say on this topic.