A few friends growing up had dogs come home limping from a .22 or birdshot. We assume they got into one of the neighbors coops. Mine learned as a pup to leave chickens alone. I don't think it affected his birdyness in the least. I had a harder time getting him to ignore songbirds and robins, he still points them on a slow day hunting.
Looking at this thread, it seems there are several people that say don't train them to leave chickens alone, they will lose their birdyness. Several more saying they did just that and it was not a problem. I'm interested to hear from someone that has trained their dog to leave chickens alone, and it did affect their hunting abilities.