I'd guess that the chip is dying right now.
But, and don't get me wrong here, this is what happens when you don't know exactly what you are doing.
Arduino is great because it powers people to do something they thought about without having to get a Phd or something like that and proof of that are all the projects that have come up made by people with little electronics experience or knowledge...
But there are still things you need to know, specially when creating hardware connections. It's true that the seller made a mistake (purposedly or not, is not the point), but you should have checked the resistor color code before connecting the resistors. It's an expensive lesson to be learned this way.
Also, I don't know what you told the electronics shop guy, but 5,1k is a bit too much to control a LED... you won't get nowehere near it's "safe" brightness limit. And maybe he thought (an error on his behalf) you would source the LED from the Arduino and then 7 Ohm would be acceptable (considering the resistor inside the Arduino). Actually, the 7 Ohm would be a waste... but he has to make a living.
In the end, the guy in the electronics shop made a mistake. Either because he tried to interpret your order and change it to what he thought best or simply made a mistake. However, you should have still checked the values before connecting. It's one of those things that you learn with experience... Too bad it might have cost you the ATmega2560.