The ideal situation would be for the store to provide the Bitcoin. This cuts out the need and costs of the prepaid card. As Bitcoin becomes more popular, stores will start to see this source of profit. This means your project may have a limited life as Bitcoin replaces prepaid cards.
I don't really think you will be seeing Bitcoin "stores" regardless though... At least for a very very long time. I mean hell, look at pawn shops that buy gold. Since it's stable and requires a hefty price tag, they can buy and resell for a small profit to remain somewhat afloat... but, with bitcoin I don't think you would be seeing any pawn shops or any other type of shops for that matter just sell Bitcoin. You might see more adoption of Bitcoin ATM's, which would take out the middle man like you said above... but not shops specifically buying and selling Bitcoins.