Most of the new strains of flu that come through every year originate in the farming practices where pigs and ducks are raised in proximity and on each other's waste products. Read more about it here.
http://www.sciencenews.org/sn_arc97/12_13_97/fob1.htm
and yes, the virus is likely killed by cooking but someone has to handle that food before it is cooked. Think SARS here where the initial viral infection was to cooks.
The biggest problem would be if the diseased ducks would be fed to pigs because the transmission route is from duck to pig to human. The virus mutates at each step so as to be able to infect the next host.