Barry
I don't know the answer regarding the segregation of the wounded from the diseased soldiers. Today it would be done, but 140+ years ago....
I didn't have any success locating JLM's burial site. He may be in an unmarked grave or there is also the possibility he was moved to Pontotoc County, you may want to check cemetery records there.
I did find this listing of a John L. Mathews (#185) in 1863.
http://www.rootsweb.com/~mspontot/cw/roll29.htm
Also a letter written by T.J. Matthews with a reference to John Lewis.
http://www.rootsweb.com/~mspontot/cw/letters.htm
Mitchell