Just because a dog is at a pet store, does not mean that the breeder is unethical.
It absolutely does -- it goes against every code of ethics of every single breed club in the country. The best you can hope for is that the breeder is so ignorant that they don't see the implications of treating dogs as merchandise (available to the first person who whips out a VISA, with no regard as to what their likelihood of taking care of the pup is). And that ignorance has other implications, because anybody who thinks it's fine to sell their puppies at a pet store to whoever also was not doing the vigorous health testing that all ethical breeders will do to try to weed out health problems.
Breeding dogs carries with it cradle to grave responsibility for that puppy.I've had them come back at 5 years old when somebody's life imploded on them. Friends who breed more than I do have had dogs come back due to death, divorce, or just hard times. You might get the call the morning of your mom's funeral, or the day after your husband says he wants a divorce. You take the dog back ANYWAY (or call on friends to help you out).
I will say that there are owners who know their contract says that the dog goes back to them if at any time they can't keep the dog, but who put it in rescue, anyway. That's where being active in breed rescue helps, because the rescue people will simply call the breeder and the breeder will take the dog from rescue. This is the reason I personally microchip puppies before placementwith my own information (and the new owner's as secondary information) so that if they ever get into the shelter system I hopefully will be made aware of it.
You can only do the best you can do as a conscientious hobby breeder, but it's no exaggeration to say that there simply is no way to ethically raise dogs as commercial livestock. And dogs in chain petstores are raised as livestock. And yes, that pup does deserve a loving home... but before you buy it, consider his mother in a cage in Pennsylvania or Missouri. She'll never leave that cage until she's infertile or dies. And if the orders from pet stores keep coming in, her daughters will be in the cages beside her.
Giving money to stores that sell dogs is directly profiting people who treat dogs like veal calves (and many people who feel sorry for mall store dogs would never touch veal with a ten foot pole). Your best bet is to stay out of the store entirely (not buying even a milkbone there) but if you do fall for an adorable puppy face, go in and leave your contact information and offer to take the dog off their hands if it doesn't sell, so that it doesn't get returned to the mill or euthanized. That way you will be doing the dog a favor and not helping the mills profit from it.