OP, what is not made clear here is there is a difference between OBDII codes and Manufacturer (BMW) trouble codes. Only the BMW codes will show indication of a failing water pump; there are no OBDII codes for a failing water pump. BMW codes are only readable by a BMW scan tool, of which various types are discussed here. If you plan on DIYing your car, get a BMW scan tool. When dealing with failed electrical components, generally one of the first steps is to clear the trouble code before exchanging the component.
Now the dealer could have been BSing you, but who knows. 39K seems a bit early for a WP to go, but maybe age is also playing a part here in the failure.
Oh, and drive your car more! 39K in 8 years is a bit on the low side, don't you think?
