A conscript was in modern day terminology, a draftee. If the index states that he was a "Georgia conscript," it likely means that he reported for duty at a conscript camp, but that no record exists of his service at a permanent unit. Because so many records are missing for Confederate units near the end of the war, it does not mean that he was never assigned to a permanent unit, only that the record for it does not exist in the Compiled Service records.
A 1990 or thereabout publication lists the militia enrollments for many Georgia counties in 1864. If I recall correctly, the list is complete for Rabun and surrounding counties. You may very well find your ancestors name in the militia enrollments in that publication. If you live in Georgia, ask the librarian in the Georgia room for the book listing the 1864 Georgia Militia Enrollments. I'm sorry that I don't recall the name of the book off the top of my head.
A fair number of the men from Rabun County ended up in North Carolina or South Carolina units, so you might check for a similarity of names in units from those states.