Kesh, you are quite right, about the fact that a Residency Stamp/Resident Card on the passport of a non-EEA family members of an EEA national is vitally important, albeit not a compulsory requirement.
Prior to 30th April 2006, non-EEA family members of EEA national used to be treated under
255-257 of the Immigration Rules.. This practice discontinued, as it does not conform with the subsequent rules, ie 2004/38EC.
Applications received before 30th of April 2006 were treated under that rule. Those received after, are dealt with under the 5 years requirements stipulated on the Directive.
In the period leading up to 04/06, people were issued with a 5 years Resident card as opposed to the 4 years one.
The OP's partner will need to reapply for a resident card which will be valid for 5 years, and apply for Permanent Resident card a years after that, when she will be qualified.
If she wants to benefit from the fact that her husband holds a permanent resident status in the UK, she will need to leave the UK and apply for a spousal visa overseas.
To be honest Kesh, it will be a waste of time and money, as the woman will qualify for permanent resident before the time her spousal visa would expire.