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Unfortunately, the clerk is correct and there exists only a narrow exception for not running it in the paper.
The exceptions are basically to protect someone who is a victim of domestic violence and other crimes.
The reasoning behind this requirement is to put anyone on notice of the change of name. In this case, you are legally changing your son's last name from hyphenated to just his dad's name. The technical reason is that if your son has entered into a contract with anyone, has any involvement with the police or is trying to hide from his debts (seems funny for a child) there has to be a way to notify any interested parties. I'm afraid you will have to publish it . While this may not be what you were hoping to hear, it does represent the law.