My approach would be to place pads on both sides of the board, at the appropriate spacing, like bobc's depiction, and then place arc shaped slots in the pads, with the slots being 0.8mm wide or greater to allow them to be milled by the fab.
In effect, you would be using multiples copies of a footprint with a slot, with slot being an arc rather than a straight line.
The arcs defining these slots would typically go in the outline layer for the fab I deal with. The gerber file for plated through holes may need to have these slots in it too, depending on your fab.
The inner radius of the arc defined slots would need to be slightly under your final marble circumference, to allow for the plating thickness.
This would allow you to sandwich the final board between the marble pieces, and turn/grind/polish the non plated FR4 intervals between pads down to the level of the marble surface, without affecting the plating in the slots.
You may prefer to leave the plated slots as slight depressions below the level of the marble and/or fill the resulting slots with a conductive epoxy or similar, which could be coloured appropriately.
Simplest of all, if you opt for recessed plated slots for later filling with something like conductive epoxy, would be to use straight slots in your footprint, which kicad should be able to handle with no extra hacking/hand crafting required for the gerber layers.
An interesting challenge.