The populations of jacksonii in CA are decended from the ones in Hawaii, which are decended from just a few dozen individuals.
Still, they seem fine. Good looking animals all over. It's got more to do with selection and less with small gene pools and population bottlenecks.
The best thing to do is to hold back your very best animals for breeding, and sell them to people who are being selective. Very few of a clutch will survive to adulthood, and few of the males will be big and strong enough to win and defend territory.
It's impossible to do anything to impact ALL non-selectiver beeding, unless you cull most of your hatchlings or sell them ONLY to people with no breeding interests. Instead, responsible breeders should themselves be selective with their breeders. IF all good breeders were selctive, and only bred the few very best animals out of each clutch, it would do wonders for the quality of the animals in captivity.