If it's just the rears I'm assuming you have the standard non-Bose system. Also is it still present on radio and CD?
If it is then it's because the rear speakers (and sub) are driven off their own seperate amp inside the sub enclosure, which is why you still get it with the volume on zero.
It'll be an earth problem as 99% of all interference problems are, not helped by the fact that the pre-out wiring from the HU to the rear/sub amp isn't screened properly. The wiring is naked where it connects to the HU which is the closest point to the engine and I'm amazed everyone doesn't get the same problem. Easiest thing to try is earthing the HU:
If you can pull the HU out, or remove the glovebox, you can then get to the back of the HU. Try earthing the HU casing. Get a short piece of fairly thick cable, connect it to the back of the HU and then try different points on the car chassis with the engine running, HU on and volume at zero. Hopefully you'll find a point that stops the alternator whine (you will need to try different points on the chassis to get a good earth).
This worked for me when I had a similar problem with an aftermarket CD changer, and I even burned a CD with silence on it, so I could listen for the whine with the volume jacked right up.
If this doesn't do the trick then you'll probably need to investigate the wiring to the rear amp. Try moving the connector and wiring around on the top connector (multi coloured plug). The pre-out feed to the amp is the yellow part of the connector shown below:
It maybe the feeble screen connection isn't making proper contact.
If this doesn't work then unfortunately you need to get to the amp, which is buried behind a lot of trim in the boot.