I am all about soy free for everyone! It is very inflammatory to the digestive system. Maybe there is an animal that lives on soy like the panda lives on bamboo but chickens aren't that animal.
Gluten however is a protein found in grains which from what I see chickens do naturally forage from dry grasses.
I do not eat gluten because I am not a chicken! (I actually went on the GAPS protocol to heal my lupus and this really works. Gluten and all grains are problematic for human digestive systems and contribute to a leaky gut which promotes many diseases that are epidemic now.)
I have no doubt diets very high in soy and any one kind of protein will affect the eggs and meat, however gluten and soy are not passed into eggs and meat in the same way as breastmilk because these are fundamentally different. Milk is essentially white blood of the mother and that is why allergens are passed to baby.
The main problem is when the chicken's primary source of protein is from soy or wheat. I like the fish meal idea. I wonder if there is bug meal out there that is nutritionally comparable? We could also argue that chickens don't naturally forage fish and sea plants either .... :)