Unfortunately there is no way to do this directly. The Eagle CAM processor specifically fills in hole areas with copper so that if there is any misalignment in the drilling stage of manufacture you don't end up with gaps in the copper next to the hole which could cause problems in the through-hole plating step and during assembly.
I understand for home assembly it would be a useful feature to create self-aligned holes, but there are no options in the CAM processor to do it. Even the DXF export ULP has the same behaviour (fills holes).
You can do it by printing the design to a PDF showing only the copper layer. This does result in the holes showing up as unfilled. However this is only useful for home chemical etching using say the toner-transfer method. I don't think there is a way to import the PDF into Freecad for milling.
You can get creative in eagle and redesign all your pads to be made of polygons shaped with a hole in the middle and a much smaller pad off to one side, however this would be far more trouble than its worth and would likely be a DRC nightmare.