E? Hmm.. I can't find the new booking/fare class list.. but I had a flight over the weekend that was originally a W fare I bought on the web... Then I called to ASK if I could cancel the return as I might fly somewhere else... The rep canceled the booking entirely by mistake and had to re-issue it.. The new record locator indicated (as well as the tickets) class "E".
I was upgraded automatically as a CP, if that helps... So its not a non-upgradable fare..
So, that was more informative to others than your wife's situation. If she has miles she might try calling now to upgrade (10-30k miles each way depending where to where), or, she can use the new "GoFirst" program and upgrade at the gate for $$.
Regards,
Mike