Even if these animals are legitimately up for adoption and are not simply animals that the store cannot sell, I personally would not want to adopt from a rescue willing to compromise animal welfare by partnering up with a store that sells animals.
By coming into a store that sells animals, these rescues are bolstering the image of the store, and thus, making it more socially acceptable to shop there, which only sends the message to the store that it's okay to continue what they are doing and only makes it that much more difficult for animal activists to put a stop to what goes on. How can we get the treatment of small animals and the sale of small animals to stop if people will say, "Well, obviously the *rescues* have no problem with it, so why should we?"
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I would personally either consider getting pets from a rescue not associated with a store that sells animals or just not getting a pet, period.