Has there even been a case of pilot incapacitation due to food poisoning?
Pilot incapacitation due to food poisoning does appear to have occurred.

The linked question, Is it true that the pilot and co-pilot are required to eat different meals? contains this New York Times article, which describes one incident:


In Australia in 1980, the pilot of a twin-engine commuter airliner suffered from food poisoning and collapsed at the controls. A passenger revived the unconscious pilot, who then was able to land the plane safely.


(However, this may not be quite what you're looking for, as being a single crew plane, it's unlikely he consumed the meal on-board).

The article also describes a number of near misses:


In 1975 luck may have prevented a catastrophe aboard a Japan Air Lines flight  when 143 of the 364 passengers and crew flying from Tokyo to Paris became severely ill just as the plane landed for a fuel stop at Copenhagen. They had eaten omelets that were contaminated with staphylococcal bacteria. The pilots, who had boarded in Anchorage, did not become ill because it was time for their supper, not breakfast. Instead of eating the omeletes, they chose steaks.
In 1982, 10 crew members of an Overseas National Airways DC- 8, including the pilot, co-pilot and flight engineer, became ill about 35 minutes out of Boston on a flight from Lisbon. After the plane landed safely at Logan Airport in Boston, Jo Ryan, a spokesman for the Massachusetts Port Authority, which operates Logan Airport, said, ''The crew all eat different things, but the one thing they had in common was tapioca pudding.'' 
In 1976 West German health officials reported that two people died and 385 others were sickened by contaminated mayonnaise served aboard a Spantax flight.
In 1976 at least 29 passengers were admitted to a hospital in Australia for treatment of gastro-enteritis after they became sick from a meal served aboard a British Airways flight from Hong Kong to Sydney.


Note the NYT article is dated 1984, so there could have been lots more incidents since then. For example, a search of the Aviation Herald for "food poison"  brings up a number. While you need to read each one and determine if the food poisoning came from the food on board, prior to the flight, or was unconfirmed as the cause, an incident of an inflight meal incapacitating the first officer occurred in a Boeing 737-800 as recently as Nov 18, 2016, flying from Spain to Denmark. In this incident, it is stated that the crew were served different meals. 

It says: A chef subsequently informed the first officer that a part of her flight crew meal (cabbage stew) most likely was the source of the food poisoning. Because the cabbage grows in contact with soil, and since it most likely was only heated and not cooked during preparation, live microbiological bacteria might have been present in the hot meal.