Thank you for your enquiry.
Although your application for PR was refused you are still a family member of an EU national. It is a reasonable excuse that your wife was out of work because of maternity leave but it is important that she goes back to work as soon as possible because only then would she be regarded as exercising her treaty rights to remain in the UK with her family member.
If you cannot provide 5 years of evidence to support your application on the basis of your wife exercising treaty rights for the same period of 5 years then any further application for PR will be refused.
Unfortunately there is no other option under EU law. She must go back to work to have any EU rights to reside in the UK.