The correct way to do it is weld `em up.
And I'll go a bit further- welding them up is the only RIGHT way to do it. I suppose you could lead them if you know someone that can work lead, but that'd be harder than welding them up.
Body filler will absorb moisture, and since it will hang out the back of the hole, there's no way to seal it properly. The end result will be the filler will absorb moisture, swell and crack the paint, and even cause rust damage around the holes.
