American Airlines is trying to scam me

Today I had an interesting conversation with an American Airlines representative.  But first, a little backstory – in July, I booked a roundtrip flight for my wife and me to fly to Raleigh for the holidays.  Each ticket cost $404 (this is important later).  Unfortunately, my wife had an emergency (don’t ask) last week and had to get to Knoxville asap, so I booked her a one-way ticket on another airline.  The plan was that she would drive from Knoxville to Raleigh and catch the flight back to LA with me. 
But today I thought I better call the airline and just make sure this wouldn’t be a problem (and see if maybe I could even get some money back).  I explained that because my wife had an emergency, I needed to cancel her flight to Raleigh but keep her flight back to LA.  The rep told me that to do that, she needed to cancel my wife’s ticket and book her a new one-way ticket, and that it would cost me $550.  I told her that I did not understand. 
She explained that there was a $150 cancellation fee, and that a one-way ticket on the same flight cost about $800, so that I had to pay the difference between that (roughly $950) and my original ticket ($404).  I told her that I did not understand. 
She started to re-explain it, but I stopped her and told her that I understand that it’s their policy, but that it does not make any logical sense.  I explained that I booked a ticket that would take my wife from LA to RDU and back for $404.  But now she did not need the flight from LA to RDU, just the flight back.  So she had to pay NOT to fly?  She said she understood my confusion, but that is their policy.
Then she asked if I wanted to go ahead and re-book it.  I told her that while I realize it’s not her fault, American Airlines is running a scam.  I told her I’d have to think about it and would call back.
I ended up calling back and just canceling the flight altogether.  To do that, I lose $150 but can use the rest ($250 if you’re not a math major) for a future flight. 
Two more interesting (assuming you’re still reading) tidbits – first, there is a flight on United the same day from Raleigh to LA for $89 (versus $800 on American).  Second, it would have been cheaper (about $250) for my wife to book a flight from Knoxville to LA tomorrow and then just fly with me the next day as planned.  So if you’re scoring at home, it would cost us $550 to NOT fly one way and $250 to fly an EXTRA way.  Makes complete and total sense to me.