There is no requirement for a citizen to "update" their naturalization certificate. That would be like asking her to update her birth certificate. Her naturalization certificate, marriage license and other id's should be sufficient. She should ask to speak with a supervisor because this examiner is wrong. If the examiner can't resolve it and there is no other problem with any of these documents, she should hire an attorney and sue DMV.
Why is Homeland Security involved? Was there some kind of underlying fraud involved with the obtaining of the original naturalization or permanent residency? That would be difficult to prove at this time, unless someone has traced back a fraudulent provider back to that time. For instance, there has been some cases where USC's born in Texas have had their citizenship taken away where their births were registered by midwives and it later came out that those midwives fraudulently listed some births as being in the US when they really took place in Mexico.
But normally, if everything was on the up and up, you should be ok. However you might need an attorney to get it unstuck.