This answer assumes the OP is correct in describing the credit as "non-transferable". If it is possible to do so, the OP's wife should simply transfer the credit to the employer.
If that is not possible, here is an argument your wife and colleagues may be able to use. Suppose the airline, instead of the non-transferable credit, had given her cash but only for 50% of the ticket price. I assume the employer would have only expected the 50% back, not the full cost of the ticket.
She should reimburse the employer the value of what she received from the airline. The value of a non-transferable expiring credit is the product of the credit amount and the probability of her using it before it expires. The fact that the value of the credit is significantly less than its face amount is the reason airlines prefer to give flight credits rather than cash payments.
Given conference and flight cancellations, and general travel avoidance, the probability she will use it is close to zero, making the value she received from the airline close to zero.
I think she should offer her employer the option of waiting until she either uses the credit or it expires, and paying the employer value of any flights she takes on the credit. That avoids the difficulty of estimating the probability of use to calculate the value now.
If they insist on payment now, she should insist on only paying the credit's current expected value, taking into account the low probability of use. That might be 1% of the face value of the credit, if she has a one-in-a-hundred chance of using it. If she is sure she won't use it the value is zero. The only case in which the value, today, of the credit would be equal to its face amount is if she has definite travel plans, using that airline, that will use the full amount, so the probability is 100%.