According to the USDA's Fact Sheet on Humane Slaughter:
The Food Safety and Inspection Service (FSIS) is the Agency within USDA responsible for ensuring compliance with the Humane Methods of Slaughter Act.
FSIS employs a Veterinarian and slaughter line inspectors at every federally inspected slaughter establishment. The Veterinarian enforces humane slaughter methods throughout the entire plant. The Veterinarian and slaughter line inspectors observe the methods by which cattle, sheep, swine, goats, horses, mules, or other equines are slaughtered, ensure plants take corrective action where needed, and are responsible for reporting instances of inhumane treatment of animals as they carry out their primary food safety-related inspection responsibilities. FSIS Veterinarians and inspectors stop the production line if they see any violations of the humane slaughter regulations.
Indeed, this is how USDA Directive 6900.2 was originally worded.
But sources tell me that, after a meeting in Washington on the afternoon of October 23, 2003 between US Secretary Of Agriculture Ann Veneman and a group of rabbinic leaders from the OU, Star-K and CRC, along with Rubashkin's attorney Nathan Lewin and Menachem Lubinsky of Lubicom (Kosher Today, Kosher Fest, etc.), the directive's language was changed.
Inspectors hands were now tied and they could not stop the line or do anything except file a report with their district office, which then had to get permission from Washington in order to act.
It appears that the throat-ripping procedure began shortly after.