On a showroom floor, about the only part of a crank that could be damaged is a chainring, and these would more likely be bent than dented, though I guess you could dent one if you tried hard enough. It's possible that whomever you talked to at the shop just simplified the issue for you as you do sound very new to bikes.

With that said, making you wait while they order a new crank from Kona seems a bit off to me. I would have asked them to either install a good crank from another bike they have (and let me keep it assuming similar spec) or provide me a loaner of some sort. They sold you a new bike with a defect so it doesn't seem right to me that you have to let them hold it for any number of days waiting on a part to make it right.