I wouldn't worry too much about the rotting critter in your little pond. There may be several organisms in there that will eat carrion. Also, the aerobic bacteria in warm, well-oxygenated water should work fairly quickly of any bits of decaying flesh.
As to catching the goldfish and koi, do you have a deep spot or some kind of "sump" in your ornamental pond? If you partially drain to there and concentrate the fish, can you cull as needed?
Crazy option, partially drain the pond and turn the shocker heater back on? If it briefly stuns the fish, can you turn it off and then scoop out some fish?
