A major issue about the 'Confederate Guerrilla' scenario is how war weary the Confederate soldiers were. Lee's Army of Northern Virginia was melting away as it retreated from Petersburg from a skyrocketing rate of desertion and Union pursuers.
However, assuming we ignored all of that, the Confederate guerrillas run into a new problem: The exhaustion of the Confederate civilians. By 1865, the CSA had reached the breaking point. The civilians were tired of war and calling for their men to desert and come back home. The Union army was sick and tired of dealing with guerrillas and adapted several anti-insurgent tactics to deal with them. As Sherman did in Memphis in 1863, Union soldiers resorted to expelling local families from their homes (in some cases entire counties), burning settlements and arresting civilians. This would prove to be quite effective. Civilians, exhausted by the violence in their communities and hopeful of preventing Federal retaliation against their homes, lost their support for the guerrilla movement and it soon began to die out.
In conclusion, by the time the Army of Northern Virginia was desperate enough to break into guerrilla bands, the Union had already won the war.