"Can you imagine what the aftermath of the Civil War would have been like if the Confederate armies had merely been defeated on the battlefield?"

Yes I can. I believe the South would have taken the stance of R.E. Lee and denounced any "Guerilla Warfare" attempt and the South would not have gone through years and years of miserable Reconstruction.

R.E. Lee discouraged his soldiers from making life miserable for civilians on the other side. It should have been expected that the other side follow suit.