Courtney, the problem is that, like high fructose corn syrup, soy seems to be in everything. People are eating more than they think they are.
Soy is a problem in people when it is eaten in a non-fermented form. Soy oil and soy flour are the two biggest sources. Read the labels on all your condiments. I dare you to find a salad dressing without soy oil.
But like I said, by the time it goes through the bird and in to the egg, how much is a really a problem? I think it is more a health problem for the bird than a problem for someone eating the egg.
LC, the coop may be over reacting a bit, but I really can't blame them too much. Hopefully you can find an affordable replacement feed. Are their any places near you that will custom mix feed? Maybe replace soy with alfalfa and fish meal?