This scholarly paper on The Scientific Approach To Resolving Conflicts Between Veterinary Science and Shechita (L.S. Shore, Israel Veterinary Medical Association, 1999) should help in understanding the issues at hand. I found the author's closing comments to be particularly prescient:
In summary, scientific studies dealing with veterinary problems in the kosher meat and poultry industry today can be characterized as sporadic, generally out-of-date, and grossly underreported. Attempts by Dr. Levinger in Israel in the early 1970’s to develop a scientific basis for research into these problems was not continued due to lack of funding. Considering that the rapidly growing kosher food market is one of the great success stories of recent decades, this policy, or lack of it, on the part of funding agencies can at best be characterized as short sighted. This is especially so as the kosher meat industry must meet the new environmental, hygienic, and food quality requirements which will seriously challenge its profitability in the near future. [Emphasis added.]
One must ask how the Rubashkin Shechita-gate Scandal would have played out – in fact, if it would have occurred at all – if rabbinical authorities in charge of kosher supervision had followed Dr. Shore's advice.