Let's take this at face value. Obviously I can ask the patron to stay until the bill is paid. The bill is paid, as always, when the money is counted and is found to be enough.
So you get someone on minimum wage to count the pennies. At least three times to be sure. And ask them to count carefully so they don't make any mistakes. Counting 2,000 pennies will take an hour, and then at least two recounts. While the customer is waiting. They won't do it again.
After that, you ban them from the restaurant forever.
(Inspired from a story on another site, where a customer in a movie theatre wants to be really annoying, buys a soft drink for four dollars, and drops it intentionally on the floor. The manager asks someone to clean it up, with no complaint to the customer. Later he explains why he was so calm: "We made $3.50 profit on the drink. It took five minutes at minimum wage pay to clean up the mess. As far as I'm concerned he can buy $4 drinks and drop them on the floor all night long.")