It is often remarked that “hindsight is 20/20.” With the advantage of that hindsight, I would argue that you, the veterinarian, should never have let the situation progress to the point it has. You have done the farmer no favor by letting the situation slide, and you have actually allowed harm to come to the animals, their productivity, and now the farmer's (and your own!) reputation.
The lesson here is that any slippage in husbandry should be met immediately with vigorous veterinary admonishment and assistance, at least until the crisis is weathered. Hiding the evidence and doing a quick clean-up smacks of a “cover-up” and will almost certainly not work now that complaints have been tendered. Collusion in such a cover-up can only harm your reputation.
But given that the damage is done, how should you behave? I would immediately begin to get to the root of the problem, and restore proper husbandry and management. If the farmer is too distraught, preoccupied, or depressed to shoulder that burden, I would seek help immediately from his fellow dairymen, since it is not in their interest to have any dairy be anything but a shining example of proper care. Were I a dairyman, I would do anything to maintain the image of a clean industry that shows concern for the animals, long established by Carnation Farms and others (Most people see dairy farming as being benign, since the animals are not seen as being slaughtered or kept to be slaughtered). Mistreatment of cows, the “mother of the human race,” will almost certainly bring down public opprobrium on the entire industry; in particular, failing to deal humanely with downer animals can become a public nightmare for the industry and a magnet for television and activists. I am certain that the industry would pitch in and help.
In my own career, I experienced a not dissimilar situation. Some years ago, I was named Dairy Welfare Extension Specialist, and my name was widely disseminated as the person to contact about dairy welfare issues. A woman from a large city repeatedly passed a dairy farm on her way to work and saw the same sick and injured animals over a week's time. Irate, she phoned me and threatened to call the media. I, in turn, called some key producers. In a day, the problem had been dealt with and I was able to call the woman and tell her precisely how the situation had been dealt with. She, in turn, was assured that the industry policed itself, and carried the issue no further. Producers and veterinarians must work together swiftly to assure a skeptical public of their commitment to animal well-being.