There is one possible answer to this question in Douglas Southall Freeman’s biography "Lee." According to his memoirs, General Porter Alexander asked General Robert E. Lee for permission to engage in a guerrilla war and Lee refused.
“Thereupon Alexander proposed, as an alternative to surrender, that the men take to the woods with their arms, under orders to report to governors of their respective states."
“What would you hope to accomplish by that?” Lee queried.
It might prevent the surrender of the other armies, Alexander argued, because if the Army of Northern Virginia laid down its arms, all the others would follow suit, whereas, if the men reported to the governors, each state would have a chance of making an honorable peace."
According to Freeman, Lee believed he had a greater obligation to the American people, that the war was over, and that to continue to fight after such agreeable terms had been offered would be dishonorable. He goes on to argue that due to how highly regarded and respected Lee was among the Confederacy, his complete surrender motivated other members of the Confederacy to put away their guns and was a contributing factor, if not the primary cause, behind the lack of armed resistance.
But the U.S. Civil war did devolve into a protracted guerrilla war. The guerrilla war led directly to the establishment of Jim Crow. Between 1865 and 1877 when Federal troops left the south under a deal (known as the compromise of 1877) to end the contested election of 1876, there was constant if not always armed opposition to Scallywags (Southerners who supported reconstruction), carpetbaggers (Northerners who came to the South in support of reconstruction) and black political leaders who attempted to run the South and preserve freed blacks basic civil rights.
For example, in 1874 fighting broke out in Arkansas in what is known as the Brooks-Baxter War where radical Republicans and Democrats fought over the rightful winner of the 1874 governor's election. The defeat of the Republicans led to the end of the reconstruction era in Arkansas. That same year Democrats attacked radical Republicans in New Orleans in the Battle of Liberty Place which also led to the end of reconstruction in Louisiana.
Then there's the emergence of the Klu Klux Klan, a loose network of guerrilla warriors (today we might even call them terrorists), that was formed in Tennessee in 1866 and engaged in a sustained campaign of bombing, political assassinations, lynchings, voter intimidation and other actions to wrest control of the South from radical republicans and return control of political institutions to white Democrats. The federal government responded to Klan violence with the Enforcement acts, which allowed the federal government to intervene if black civil rights were being violated. The Enforcement Act of 1871 is known informally as the "Klu Klux Klan" law. The Klan was eventually defeated and a different Klan emerged in the early 20th century.
In the end, the sustained guerrilla campaign was a success. Radical republicans were purged from the state government, black voting rights were eliminated and white Democrats would have basically unchallenged control in the South until 1965, when passage of the Voting Rights Act finally resulted in the registration of millions of black voters in the South.
A good book to read about Southern violence after reconstruction is called The Bloody Shirt: Terror After Appomatox
I recently completed my BA in history. My final research paper was over the Indiana Legion. In Indiana at least there were two major "guerrilla" offensives conducted by the Confederates into Indiana. The most famous being Morgans Raid.
Morgan set a precedent , which was that Confederate sympathizer known as Copperheads could harass and raid along the Ohio River between Indiana and Kentucky. The Indiana Legion's job in southern Indiana would ultimately be to stop guerrilla warfare.
Sources: u.s. Army and irregular warfare: 1776-2007, Report of the Adjutant General to the Governor of Indiana, lots of primary sources too.