I always get nervous whenever I read the reviews about Chef Mickey's but then we still end up going every trip and every trip we enjoy it. Disclaimer - we always go for dinner, I have never been for breakfast.
Yes, there are some nasty issues with buffets, ANY buffets, in general. Does it thrill me that there are people who use their hands instead of tongs? No (I honestly have only seen this a few times and always with something like rolls, cupcakes, cookies, etc. Thankfully I have never seen anyone dig through the mashed potatoes or scoop up a piece of salmon with their grubby little paws). Does it gross me out that large numbers of people are breathing all over the food, sneezing, etc. Absolutely. But at the end of the day, at a non-buffet restaurant I have no way of REALLY knowing what my food has been through before it makes its way to the table. Being married to someone who was raised by parents who have always owned restaurants, he assures me nothing I see at a buffet is as bad as what is potentially happening in the kitchen. I just keep that in mind since I am not willing to prepare all my own meals while on vacation at WDW.
I have never gotten food poisoning or even felt ill after eating at CM. I know several people who have felt sick after eating at buffets at WDW but I'm guessing that's because they went for the "All You can Eat" factor and then headed out to a nice humid, 95 degree day in the parks.