If you have a digital camera, it is probably a good idea to take documentary photographs at the store when dropping item expensive and delicate item off for service. That's like when you rent a car any they go over the car with you, noting any pre-existing damage before you drive away. That protects both them and you.
In this case, the store is taking temporary custody of your MacBook, so the roles are reversed, but the concept is the same. I'd make sure the work oder slip makes note of any damage - or general condition of lacking damage when handing over the computer.
It is a hassle, but at this point, Applecare and customer relations are probably your only recourse. At the very least, if you notify customer relations, perhaps they will put pressure on the store to handle equipment more carefully and future customers will benefit too.
This thread bothers me. Several other discussion threads recently reported similar poor experiences at Apple retail stores: either carelessly treated equipment or bad advice / crass treatment by the so-called geniuses. I want to see the quality of the Apple stores to be kept high, as this is what helps differentiate Apple from being just another PC. I feel the differentiation is part of what keeps the value of my Apple stock shares high - and I like that. (So far, there's a lot to like!)
Bill