The clerk of the court is correct. Writing a check that you know cannot be honored because of insufficient funds is a crime; stopping payment due to a dispute over the work is not a crime. The business can sue you for the money, if they believe they can prove that the work done was acceptable and so you should have paid for it, so they could (if they can convince a court of that) get the money from you, but they you should not face charges or criminal liability.