If it brings you moral discomfort, why do you shop at whole foods? Shopping at Walmart (or whole foods!) would also bring me moral discomfort, so I just ...don't do it.
Whole Foods has the food products (produce, dairy, eggs, grains, nuts) that we eat, is cheaper than the competition for this stuff, and unbelievably beats the co-op on labor relations. However, it also ships profit out of the area. For now, it's sort of the best of a bunch of not particularly good choices.