You shouldn't have to pay the fee at all - it's not a pay and then get reimbursed situation. It's supposed to be completely waived if you are a cardholder as long as 1) your AA number is in your reservation at least 7 days before departure and 2) it's a wholly domestic itinerary.

I think if I were the OP I would have your wife start with a claim to AA for a refund of her charges. I'm not familiar enough to know if your daughter's bag fee should've been waived as well.