If you're in a professional ag setting (farm, etc), that small amount of milk (and even smaller amount of antibiotics in said milk) should pale in comparison to the amount of material in your compost setup. Should be fine, although I'm willing to test this theory out.
Disclaimer: I'm not a farmer, but I do manage the IT/automation of my/a family farm.
This seems like exactly the kind of "slowly and steadily select for antibiotic resistance in bacteria" behavior that they're trying to avoid with these changes.