$1,000 really isn't bad. The parts for rotors and pads & sensors will run you $600 or so, and a full brake job will take a couple of hours, so it's really only about $100 per hr labor which is reasonable. I do brakes myself (it is easy but messy) so I don't pay for labor.
EDIT: Just to clarify, you want to buy OE pads that are not in the BMW box? Go on ECStuning.com. They are a supporting vendor here and they can help you with this.