On car lathes skim the discs, but the lathe is attached to the hub, so it should mean it is perfectly tailored to the car. If you took the disc off and skimmed it and there was slight run out in the hub, the same problem would come back.
Have a look here...
http://skimmydiscs.co.uk
It's not that cheap, so if the discs aren't that new it probably isn't worth doing, rather have new discs fitted... the first should be able to make sure any run out is compensated for.
I should warn you, I'm no mechanic, so I could be barking up the wrong tree!