Assuming there will always be some occasion where the food tested will not be cooked properly, what method is used to prevent cross contamination?
Most of the time, an instant read thermometer is wiped with a towel. Remember, these folks do this every day, all day. In kitchens where they are used (they are not used everywhere...they are required in some kitchens), the tested product is probably in the ball park. Most pathogens are reduced to safe levels once a product hits 140F (60C) using traditional cooking methods. They are generally testing cooked food. Though, on the occasion (and it is probably rare) when raw protein is tested, the end of the instant read thermometer can and should be washed in hot soapy water. In a professional kitchen, it should also take a dip in a sterilizing solution.