I have had reasonable luck getting the call center to waive booking fees for itineraries that cannot be booked (or upgraded) online.

The Premium Team seem to have this power - and while they may not offer it at first, if you ask for it they will usually do it.

I've done this a few times since 2006, including getting Travelcentre to waive the $100 booking fee; most recently with the call center about 3 weeks ago.

Edit: The one thing they won't/can't waive is reissue/rebooking fees (unless due to their error). Clearing a wait-list at Christmas meant an AUD$20 reissue. The agent apologised for not being able to waive it.