There is a great deal of irony in Peyton Farquhar's agreement with the idea that "all is fair in love and war." It is evident that Farquhar does feel that he is justified in doing whatever he is able to support the Confederate forces, since he is unable (for whatever "imperious" reason) to actually serve as a soldier in the army. This is evidenced by the actions Farquhar takes after ascout working for the Federal army tricks Farquhar into believing he is a Confederate soldier and is giving him useful information.
The irony of the situation is found in the fact that Farquhar is hanged, in essence, for doing what he feels is needed. Farquhar feels that it is fair to attempt to burn a bridge to block the progress of the Federal army. According to his belief in fairness, he must also believe it is fair for the Federals to hang him for his attempt at sabotage. Based on the notion that "all is fair in love and war," Farquhar could not even argue that he did not deserve to be executed for his actions.