Well, no reputable breeder would EVER sell their dogs to a pet store so anyone who thinks that a pet store dog is from a reputable breeder is highly mistaken. A reputable breeder will screen all of their potential applicants and and make sure that the dog is going to the proper home.
Don't get me wrong, I have made the mistake as well and bought my dogs from BYB's. I have since learned a lot about BYB's and puppymils and know that any dog I get from here on out will be from a rescue or shelter. I know that the past of these dogs might be unknown but it is a fact that for every dog purchased from a BYB or puppy mill, 3 dogs are killed in shelters due to the over population problem.
You are correct in saying that it is not the dog's fault where he came from and yes, he does need a home but by purchasing from the pet store, you are directly or indirectly supporting the mill or BYB because you are funding the store to purchase more animals from them to make a profit. If you do not draw the line, how will places like this ever be shut down. It's all about supply and demand and if the demand is not there, these horrible places will be forced to close.
A reputable breeder will breed his dogs to better the breed, or to continue champion blood lines, not just because they have a cute dog and think that they would make cute puppies. Reputable breeders are not just in it for the money.
I won't even buy anything from a store that sells animals because that also helps them support BYB's or mills. Any profit that they make is only going to end up going towards things I do not agree with.
Here isjust one of many articles regarding pet store dogs:
http://members.aol.com/KARENKATO/petstore.html