I don't have a problem with "pet stores" per say either. For many there is no other source of supplies or animals near them and when you first get into the hobby, i.e. when you get your first gecko, snake, etc. you may not even know that shipping is possible. I know that I started out with a couple crested geckos from petco. Were they from a big box store? Yes, but they were also well-cared for due to the store having an experienced herp person working there.
I think that saying stores should not sell reptiles would greatly decrease access to the hobby and would probably lead to less people becoming keepers.
I'm not defending bad husbandry, however, and yes it is best to buy from a local shop that has good conditions. But there too, I've seen many mom and pop stores with worse conditions than the big box stores.