Oh no, I'm sorry to hear your friend got sick! After reading through this thread, it sounds like some people have an allergy to duck eggs... maybe that's his problem. Because it doesn't really sound like salmonella poisoning... from WebMD: Symptoms of salmonellosis include diarrhea, fever, and abdominal cramps. They develop 12 to 72 hours after infection, and the illness usually lasts 4 to 7 days.
We've been eating organic store-bought chicken eggs over-easy for many years and haven't gotten sick yet. Our ducks are too young to produce eggs yet, but I ate a duck egg from a friend (intended to cook it over easy, but it was totally undercooked because I was used to cooking little chicken eggs)... anyways I ate it without getting sick.
The risk of salmonella in eggs is much lower for pastured birds (yours) than battery farm birds (the grocery store's). I recently read this article (if you google "Empowered Sustenance raw eggs" you'll find it) which says that if you eat a battery farm egg raw, you have a 24% chance of getting salmonella. If you eat a pastured egg raw, you have a 4% chance of getting salmonella.