That depends on whether or not it is a false-positive or, pardon the saying, a legitimate pirated copy. Probably the best first move is to call Microsoft's activation hotline, explain the situation, give the person on the phone your product key, and they should then be better able to tell if it was incorrectly flagged. If it was, they can issue a new activation code over the phone for you. If not then you're SOL and have to buy a new copy of Windows, though you won't necessarily have to reinstall, you should be able to activate the existing install using the new product key.

I wouldn't get my hopes up, but it has been known to happen that Microsoft will throw free copies of software at people who report businesses installing pirated versions of their software. If it turns out to be a legitimately flagged key, I'd turn in the retailer without a second thought, maybe even consider taking them to small claims court for the cost of a new copy of Windows and whatever they might have charged me to install it, if you don't mind them banning you for life from the store. They defrauded me in this situation, and so all bets are off as far as I would be concerned in that situation.