I think you are misunderstanding the situation. That is, they simply can't do "it" (no matter what "it" is) if the computer doesn't allow it. They don't have the power to override. In fact, based on some issues I am having with a reservation, even the senior people are limited in their abilities. (I changed a 2 night MARRIOTT award stay to a one night stay. Marriott res couldn't do it, but they called the hotel and the hotel confirmed that they would accept the change. That is all documented in the notes. But I have been on the phone with Marriott reservations for over 35 minutes while an agent who AGREES works with her tech support and her lead agent and they haven't yet been able to actually change the reservation in the system so that I only get charged the points for 1 night, instead of 2.)
Do I think this is acceptable? No. But put the focus where it belongs - on the management/IT side. The agents don't care what the T&C say because it doesn't matter to them - if they don't see the inventory they can't book your room. You need to redirect the request to management.