Actually I think i've answered my own question! Did some deeper googling and found this post
http://photo.net/digital-darkroom-forum/00MMhy - basically, as long as i'm shooting in RAW, the White Balance setting is only going to really effect the preview on the back of the camera, and that's about it - as it wont be applied to the image (as it would with a JPEG) when saved to the camera.
Does that sound right? Any other tips to do with night sky photography would be much appreciated!
Thanks!