Hopefully not... at least for contract fares, the tickets are booked into a published fare basis (with restrictions on the payment method). At least for us with SATO, both the charge and any refunds on the credit card come directly from the airline and the service fee is separate.

If I want to take a personal side-trip from a work trip, my agency requires us to ticket the official itinerary and then change it (seriously!), so I always go straight to the airline (sadly, now that I'm in California that usually means calling UA in India) and let them sort it out. That also allows me to pay the difference directly out of my pocket and not have to hassle with making sure I can show my work and prove I'm not charging Uncle Sam for my vacation.