In these cases, you are much better off bypassing the front-desk folks and going straight to the service manager. You know and he knows that the extra labor charge to put in a pump that YOU supplied during a t-belt change should be 1/2 hour max, and he will likely relent as long as you keep pushing when he says no and you keep saying the same thing over and over again. As soon as you walk, they win. If you don't, they don't. If you are sure that they shouldn't have charged you $250 for it (and you should be!), he will realize it and will likely relent. Give him the necessary suggestion: "Considering the amount of work you did, how long it took, and the size of the bill, I want you to discount $200 for the installation of the water pump as a courtesy to a good customer."
It is better to fight a battle on the front lines (in front of the service manager who can alter the bill) than from the rear (through the BBB). If that doesn't work, THEN go to the BBB.
Good luck!