Which side does Peyton fight for?

Peyton Farquhar fights for the Confederate States of America (the South). Readers get this information from a couple of different points in the story. In section 1 of the story, readers are told that a man (who we find out to be Farquhar) is being hanged by the "Federal army." Readers are likely to assume that if the Union army is hanging this man, then the man must be a Southern sympathizer. I suppose it's possible that the man could be from the North and is being hanged for treason; however, section 2 of the story clearly tells readers that Farquhar is a Southern planter and slave owner from Alabama.
Additionally, readers are told that he was an original secessionist and devoted to the "Southern cause."  

Peyton Farquhar was a well-to-do planter, of an old and highly respected Alabama family. Being a slave owner and like other slave owners a politician, he was naturally an original secessionist and ardently devoted to the Southern cause.

A bit later we find out that for some reason, Farquhar was prevented from joining the Southern army, and he has always been upset about that. He longs to find a way to take action against the Union army for his beloved Confederacy.

Circumstances of an imperious nature, which it is unnecessary to relate here, had prevented him from taking service with that gallant army which had fought the disastrous campaigns ending with the fall of Corinth, and he chafed under the inglorious restraint, longing for the release of his energies, the larger life of the soldier, the opportunity for distinction.