you would have to use a mill with a large siezed bit. but milling a disc is unrealalistic due to the following
1. lets say a disc rotor is two mm thick. if you sat the disc on a perfectly flat surface and measured the amount the disc was warped (lets say it was point 25mm out) you would end up having to take half a mm off the thickness of the disc (a whole damned quater) deaming it unoperable anyway.
2. even with the biggest industrial (of course bigger ones can be made) size available for mills (wich as far as i know is about 200mm) the surface area of the mill bit would create enough heat through friction that it would end up warping it as soo as you stoped milling.
with that in mind its probably easier to use a lathe (the holes wouldnt be any probly providing you worked in small amounts) but that to is unrealistic since the preasure aplied on rotor by the blade would warp the rotor just as much as the mill but in a different way. p-out
correct me if im wrong my knowledge on tool making is still growing