Call the police pronto!! If you tell them the pistol was stolen, defaced, and subsequently recovered you will have a defense in case the gun is ever brought into a criminal case or if someone finds out the pistol has no serial numbers. Then the authorities will know that it wasn't you and the report will be on file. They will also know not to charge you with a felony due to the ground off numbers. However, if you don't report this, none of this will go on file with anyone that will have any sway with the courts and if the day of reckoning comes, you'll simply look like guilty criminal scum making up a classicly overused excuse to get himself out of trouble. If you report it, the police will get this knee jerk urge to charge your stepson. You can tell the police you simply want to report it and don't want to press any charges but the D.A. has the authority to over rule you and file charges on behalf of the state against your wishes.
Also, take this as a sign that you need to spend some time with your stepson and gain a best friend before you loose a son. This is a classic sign that he's starting to "fall in with the wrong crowd". I just hope it's not too late.