Gold Filled is a little fragile so you don't want wear away the gold layer with any abrasive method.
If you bought them from my Rings & Things I'd suggest sending them back for replacement and so we'd know our stock had rough edges. Is this a flat disc or does it have a hole in the middle making it a bead? Is the rough edge on the outside edge or around the hole? If I understand your description it's not a bead.
If you have a steel or agate burnishing tool (the kind you use to push down a bezel around a stone or to burnish metal clay) you might be able to round over the rough edge. That would mean doing them one by one.
Just a thought... is this single clad gold filled? That is, is one side gold with the back side brass? And the rough edge on the brass side. If so then your dremel with craytex tip used at an angle woud take off the rough edge. Using it at an angle would avoid removing the gold from the top surface.