As an update, I tried calling EVA airlines, the operating carrier, but the EVA phone agent couldn't give me an answer and just said "WE advise changing the ticket." When I asked if she could fly with the documentation I mentioned. He put me on hold for a while, then the call dropped.
The problem here is the ticket is booked using Avianca frequent flyer miles. EVA says they can't change the name because Avianca issued the ticket. Avianca says they can't change the name on the ticket at all.
So they only options are (a) cancel the ticket, pay a $200 fee, hope the frequent flyer seat goes back into inventory and that the miles are reinstated quickly and she can rebook to fly with us, or (b) roll the dice and show up with the documents at the airport and see what happens, or (c) try to get some assurance in advance from EVA that they will accept her US passport in a different name.