Just before Robert E. Lee's surrender in April 1865, General Porter Alexander knowing of Lee's intentions to surrender proposed instead that the troops "scatter into the woods and hills".
What would have happened if Lee had agreed to this, or at least gave over the command to Alexander?
Would there have been a full blown insurgency? How long would it last? Would the South be fully occupied by Union troops? Could the Confederacy rise from defeat?
Nothing much. By 1865, even most pro-secession Southerners were worn out and ready to surrender. Lee's own men were exhausted and starving. Thousands had discarded their rifles, leaving them spiked into roadsides by their bayonets.
And there was never more than a plurality for secession, except in a few hotbeds like South Carolina. In many areas, more people opposed secession and were coerced by the secessionists. In all areas there was a large element that had no opinions, and either wanted to be left alone or was temporarily stampeded by the secessionists in 1860-61.
By 1865, these groups far outnumbered the remaining secessionists, and they would not support, would in fact oppose Confederate guerrillas.
Then where would the guerrillas operate?
In the mountainous areas of the South, the people were largely Unionist. They would help the Yankees or hunt down the Secesh themselves.
In the broad plains, half the population (often much more) were black ex-slaves. No guerrilla movement can survive in an area where most of the population opposes it. Even if the blacks did not take an active part against the guerrillas - they would be everywhere, see everything, and tell the Yankees.