I've worked in a couple of different game chains - I'm a high flyer, me - and they all gut to some extent. I wouldn't be too worried about the state of the boxes, but how the disc itself is treated afterwards varies to a huge degree. One chain I worked for put them in little cd sleeves, another simply elastic-banded the disc into the manual, and another shrink wrapped the disc into it. Of those, the latter option was the worst, it gives the disc itself enough room to float around in the manual and get scuffed. Banding is fine on the disc, but can make the manual look weird, and the CD sleeves are alright but absolutely guarantee you will never find the game your looking for when you need to.
It's worth asking for a mint copy if you're picky about that stuff, but by and large the gutted copies are the last resort anyway, so if they're giving you one of those, there probably aren't any wrapped copies left. 99% don't give a crap, the other 1% can be incredibly unreasonable about it.
Gamestop was pretty much the only chain I never worked for, but my experience of them as a customer would suggest that there is a huge inconsistency in quality of service from store to store. But as with anywhere else, it's all dependent on how much of a douchebag the managers are, and for whatever reason, Gamestop seems to hire an unusual proportion of douchebag managers. I don't know what kind of adult feels the need to chew the head off their employees in the middle of a busy store, but speaking a customer, I cannot believe how often I've seen it happen in Gamestop stores. That's my single biggest complaint with this store - their employees aren't always well informed, but so long as they get the job done, I don't mind. I sympathise with them, in fact. But nothing will send me running out of a store faster than seeing that kind of management bullying. It's just unnecessary, and it's a disgusting way to treat people just because you can.
I'm interested to see what "Ben" might have to say re: insurance. I'm not overly familiar with the Gamestop system, but I don't enjoy that part of any sale. I love games, I know what I'm talking about, and I don't mind saying I am a great salesperson, but that bit makes me feel like a con artist.