Without getting into the rest of the issues, let me tackle the fish feed as I believe that the argument about using wild fish stock to feed aquaponic fish is a bit outdated. There are at least a couple of resources available now that sell USDA organic fish feed which is certified to have no fish meal or soy.
The rub is the cost, which at around $3/lb is at least double the conventional feed.
Please see: http://www.theaquaponicstore.com/AquaOrganic-Organic-Fish-Food-s/126.htm
From the latter (and no, I don't necessarily know what I am looking at, so if someone with more knowledge can point out other "gotchas" please pile in)
Crude Protein (min) 32.000%
Crude Fat (min) 4.680%
Crude Fiber (max) 8.700%
Lysine (min) 1.700%
Calcium (min) 0.700%
Calcium (max) 1.200%
Phosphorus (min) 0.400%
Ingredients: Organic Wheat Middlings, Organic Rice Bran, Organic Canola Meal, Organic Corn, Organic Linseed Meal, Dicalcium Phosphate, Lactobacillus Acidophilus Fermentation Product, Reed Sedge Peat, Monosodium Phosphate, Magnesium Oxide, Sodium Sulfate, Manganous Oxide, Folic Acid, Niacin, Choline Chloride, Biotin, Riboflavin, Vitamin A Acetate, Vitamin B12, Vitamin D3, Vitamin E, Calcium Pantothenate, Ethylenediamine Dihydriodide, Beta Carotene, Pyridoxine Hydrochloride, Ascorbic Acid, Yeast Culture, Thiamine Mononitrate, Ferric Choline Citrate Complex, Organic Dried Kelp, Zinc Amino Acid Complex, Cobalt Choline Citrate Complex, Salt, Copper Choline Citrate Complex, Manganese Amino Acid Complex, Potassium Chloride, Attapulgite Clay, Organic Fenugreek, Organic Grape Seed Extract, Organic Lecithin, Enzyme Product, Organic Aloe Vera Juice, Calcium Carbonate, Sodium Selenite, Citric Acid, Calcium Hydroxide, Copper Sulfate Pentahydrate, Zinc Sulfate Monohydrate, Manganese Sulfate, Organic Garlic, Diatomaceous Earth, Silicon Dioxide, Organic Dried Whole Milk, Organic Sugar, Potassium Citrate, Calcium Sulfate, Magnesium Sulfate, Activa Natural Source Mg, Fe, K, Organic Potato Starch, Organic Dry Whole Egg, Organic Tomato Powder, Organic Sources of (Orange Peel Powder, Cayenne Pepper, Dandelion Root, Dandelion, Cloves, Sage, Peppermint, Fennel, Hops, Parsley, Thyme, Lemon Grass, Elder Flowers, Chamomile Flowers, Licorice, Basil, and Ginger), Fumaric Acid, Organic Oat Groats, Yucca Schidigera Whole Plant Product, Organic Water Extracts, Organic Gelatin, Iron Polysaccharide, Copper Polysaccharide, Magnesium Polysaccharide, Manganese Polysaccharide, Zinc Polysaccharide, Zinc Sulfate, Pectin, Granite Dust, Perfect Food Berry, Ferrous Sulfate, Zinc Oxide, Sulfur, Organic Rice Protein, Copper Sulfate, Yeast, Cobalt Carbonate.