You may have unwittingly saved the rest of the flock by killing a sick bird.
I have a simple rule with questionable foods. Don't eat it! (If you have any other option).
Years ago I used to trap cottontails in Southern California. I would butcher them out in the field and bring the meat home for my mom to cook. Occasionally I would find a rabbit with some kind of growth or bubble in it's gut cavity. I left those carcasses out in the field.
I was raised with the idea that if you kill it you eat it, but there were always unspoken caviats. You don't have to eat mice you trap in the house, or skunks or other varmints you kill out of neccessity. And you don't have to eat sick animals!
A leading theory is that ebola entered the human population from people eating sick primates. (I think no one really knows, or can ever know how such things start). With a few notable exceptions, diseases rarely cross species lines (the more the animal is like you, the easier the disease crosses, which leads me to wonder about the several diseases crossing between pigs and people, then I realize convergent evolution can get marsupials to a dog or wolf like shape (tasmanian tiger), I've been called a pig a time or too, hmmm....) Wandering off subject!
I guess my advice would be, you can still raise and eat animals, but I err on the side of caution with sick animals.