If you think it was an honest mistake, you want to build a relationship with the yard that will pay dividends over time, and would have ultimately done it anyway, then pay it, full fare. Be happy with the outcome.
If on the other hand, you smell a rat as I do, then this is not a yard that you should build a relationship with. Not only should you not pay it, you should make plans to move to another marina for all of your business. The fact that most people not only put up with this, but in many ways encourage this kind of behavior due to their weak mindedness is the reason you won't be another willing victim.
If they want to file a lein, let them. With your unsigned work order, you can inflict damages on them if they try to go after you. Shout it from the rooftops if you need to and sue them for damages, hoping they make the move to try to impound your boat.
In summary: No dickering smile wearing if they made an honest mistake, scorched earth if it was a ploy. I vote personally for scorched earth.