You are applying under EU Directive 2004/38 route as the resident of an EEA country ( NOT as a UK citizen).
So you need to meet the conditions of the EU route.
The point you raise is a good one and has been argued over at a lot of tribunals.
Basically, they have come to the conclusion.
1. you the EEA national - if you are not economically active such as self-sufficient or a student, then you have to be able to financially support the family members you sponsor and have CSI for EEA and family members.
2. Then, if you met those conditions, the non-EEA THEN has the right to work, cos you are exercising Treaty Rights.
That must be the order of things.
The UKBA and Immigration judges say if the conditions listed in 1 have not been met, then 2 does not apply.
Thus, any work and any earnings by the non-EEA are unlawful and disregarded as proof of self-sufficiency.
So, if the EEA national is relying on unlawfully obtained funds for proof they are exercising Treaty Rights as self-sufficient, then UKBA will reject any application for Residence cards or PR.
I also explain that here:
Personally, I don't see what practical difference it makes, if you aren't using public funds, but that's the UKBA and immigration judges for you.
UK citizens do not require a residence card as they automatically have all the rights to enter UK, work etc. A residence card would serve no practical purpose.
My personal opinion is you will not meet the criteria for Treaty Rights so they will reject the non-EEA's residence card application and try to cause you problems, so tell UKBA nothing and do not apply UNTIL you have sorted out your situation. Simplest way is get a job for at least the time while applying for the Residence card for your non-EEA spouse.
If you aren't working again, five years down the line when you apply for her PR, then the same situation will arise.
Maybe another option is keep your heads down and stay as you are, but the lack of a residence card could make it hard for your non-EEA to return to the UK if she ever goes abroad and possibly problems in proving right to work etc. But that needs further thought.