Batman has Lucius Fox man a device that monitors all of the cell phones in Gotham to give Batman an edge in his fight against the Joker. Fox is so against using this device that he says he will resign afterwards if Bruce asks him to use it. Why was this device so dangerous in the mind of Mr. Fox?
Fox believes this device, while in existence, is more evil than the Joker.
This is due to the nature of turning every cell phone, something we can assume every citizen in Gotham owns, into a sonar device capable of mapping the immediate area, spying on every single person in Gotham.
This scene shows Fox's true ideals of being a proponent for individual rights and against spying on people for information. Bruce, however, is desperate enough to put Fox through this stress in order to catch the madman that is the Joker.
This is alluded to by Alfred when Bruce asked how his platoon caught the thief. He stated that they simply "Burnt the forest down". This is Bruce's forest fire, tearing down the walls of Gotham for him to find the Joker.
However, Fox's faith in Bruce gets rewarded, as he enters his name into the console, the machine begins to overheat and self destruct, proving to Fox that Bruce merely needed this cruel and potentially dangerous tool to find the Joker, and for nothing more.