Destroy the deformed fry. No sense letting it grow up with a problem you can't correct. Feed it to another fish so he can live through it. 

Even if they're all related, a brother-sister cross will create more problems than crosses from distant cousins. Keep the fish you'll house as your own, but... you've talked with other breeders and you've looked at the conditions and food. If you're still getting such a high percentage of deformed fry, then you know now it's got to be a real bad genetic trait in one or both of the parents. If you go on breeding them and selling the offspring that don't show an obvious deformity, the genes are still there and you are very likely doing a disservice to anyone else who breeds from those fish.. perpetuating even more problems for this species down the line.