I just tested using a quarry on each of the ores that Galacticraft adds plus meteors. It seems to me as though they are all working correctly.
Ores like copper, tin, iron, etc. just drop the ore blocks like they are supposed to including cheese ore. Meteors, desh ore, and silicon ore dop raw meteoric iron, desh ore, and raw silicon respectively when they are mined with a quarry, also like they are supposed to.
All items dropped that need to be smelted also work correctly and smelt when placed in a furnace (e.g. moon tin, mars copper, raw meteoric iron). Cheese ore even smelts if picked up with Silk Touch.
So the only ore that cannot be smelted is silicon ore, but it does at least drop raw silicon when mined with a quarry. So as long as you don't pick it with Silk Touch you SHOULD be fine.
Now are you saying that a quarry doesn't drop raw silicon? Or just to make it able to smelt, regardless?