I just wanted to take a moment to let other researchers know that I have completely revised my stance on this family and the relations within, based on evidence I have gathered from numerous records over the intervening years. I didn't want to delete the original post, however, because it still has valuable, factual information in it.
That said, I now believe that Samuel was married only once, to Sarah McKinney, daughter of Charles McKinney of Buncombe Co., NC. The Samuel Hopper who married Elizabeth Murphey in Caswell Co., NC, appears to have been a completely different person. Sarah was most likely the mother of all of Samuel's children. I have several records related to the probate of Samuel's estate in Rabun County, and other records created during his time there.
I also do not believe that Samuel was a son of Thomas Hopper Jr. In fact, I think it more likely that he was somehow related to the Charles Hopper family of Burke Co., NC, who spread out into Tennessee and other parts westward.
I am still researching this family, and would still like to discuss the research with others.