Why not use a ticket system ?
Toys 'r' us have been doing it this way for years.
There are loads of ways around it.
No way does a shop 'need' to put the real cases out on display.
For what it's worth, Sainsbury's don't do that; customers don't like it and it increases the chances of discs, manuals etc going walkabouts. We either use SWOP cases (dummy cases which we then exchange for the sealed product at the desk), or in the case of cheaper titles, the security safe-cases with the 'live' product inside.
Game always put 2 'real' cases on display which means they are always the last 2 to be sold.
That doesn't make it a good idea. Obviously with a games retailer a ticket system wouldn't work so well, but there's no reason they can't use dummy cases, and no excuse for selling games in such a shoddy condition as 'new'.