Firstly, your son should plead guilty to this offence. "No Insurance" is what is known as an �absolute� offence. It is the driver�s responsibility to ensure (absolutely) that he has a valid insurance policy. If he has not he is guilty of an offence, whatever the circumstances.
He should go to court and plead guilty, and explain the circumstances. As you have probably discovered, the offence carries a minimum of six points and there is generally no way round this. As a �new� driver the DVLA will automatically revoke his full licence and he will revert to provisional status. (The magistrates have no say in this matter. It is done by the DVLA when they are informed that the driver has accumulated six points).
The only hope your son has of avoiding this is to ask the court to impose a short disqualification (perhaps 14-28 days) instead of the points. Strangely, a disqualification does not lead to the revocation of the licence.
Although the magistrates have the discretion to do this, they will need persuading as they are effectively increasing the sentence beyond their guidelines without just cause. This is especially so as presumably the new Certificate of Insurance clearly had an expiry date shown. It would be a good idea to employ a solicitor to put his case. He will be able to fully explain how your son came to be without insurance and link the probable consequences of six points to his employment prospects, etc.