Sounds like someone who is knowledgeable and credible about water runoffs/flooding needs to get involved. Perhaps they may be able to help you convince the authorities issuing this, that their fix isn't the right one.
...and if it is backing up as a result of the pond, wouldn't adding a larger spillway be the solution. Just because you dig the pond deeper, doesn't mean that it will hold more water at runoff times. That would only help if the water level was lower before the rain. I get a kick out of people(and counties) who dig an already water filled ditch out deeper, thinking that when it rains, it will solve the problem of the ditch flooding over the banks!!!
