Ahhh, I understand.
I would suggest if they are paying $500 for a one way that doesn't earn miles show them you can probably fly for less on a restricted ticket anybody can get online and save them money, and earn you the miles. Do the math out to show how many times you have actually had to change a ticket once it was issued, and if it's not at all then you should easily win the argument.
We had a similar situtation with a company I worked for, everything had to be through the inhouse agent and nothing was cheap. I would get pricing from them, look it up online, and show the same city pairs on the same airline could be had for $350 instead of $1500, and it wasn't much of an argument that either the agent had to book the $350 flights or they were gone. On top of the $1,500 they wanted to charge us $25 for screwing us.
If they have negotiated fares that you can not get on your own, then I think you lose this one, but if they are not getting better fares then you can, they would be foolish not to listen.