If I've ever had anything close to this happen at any GS I've been to, it was never to that extreme. Some of the stores around here even go out of their way to keep the original case/manual/etc intact for used games, but they can't help if the person who trades one in gives them an incomplete copy. Finally, I've only ever had them give me the *best* copy of a disc they had available, without having to even ask.
The only thing I'd wish was done was for their electronic inventory to track whether a game was "complete" (case/manual/etc) or not. This could be a simple check box(es) that the employee marks when taking a trade in so that a future buyer who is browsing their local store's inventory online for complete copies knows whether the trip to the store is worth it.
As for the militant upselling, almost every corporate run store puts this requirement on their employees, and I've learned to just tune it out. Sure, this guy got a bit overzelaous, but maybe he had just been disciplined for not doing it at all.