Well, look at The Troubles. The PIRA guys were basically guerillas par excellence, and after striking deals with Gaddafi and his ilk abroad, they acquired some pretty decent equipment. Mind you, military-grade modern equipment : Rocket launchers, submachine guns and assault rifles, decent supplies to make a lot of explosives and bombs. And, despite all that infrastructure, effort and terror, their ultimate objective of scaring the British into giving away Northern Ireland didn't succeed and eventually wound down with a barely audible whimper.
Now, imagine the Confederate equivalent of Latvian "forest brothers" or German "werwolf"-s, equipped with 1860s/1870s technology, with probably low numbers and low support due to the CSA population being fed up with the war and the freed slaves being double unwilling to join any CSA-recreation guerillas. Compare the size of the former CSA with that of Northern Ireland. Do you think those volunteer CSA stalwarts could achieve what even the PIRA and offshoots at their most succesful didn't manage to achieve at all ? These CSA resistance guys wouldn't be exactly like the pan-nationally united Spanish guerillas from the times of the Peninsular War. Yes, those 19th century guerillas wooped Nappy's arse with even older firearm tech and common sence cunning, but their motivation, background and inside/outside support was distinctly different.
Also, pissing off the reconstruction era Union government with repeated guerilla warfare will probably not bode well for the armed movement in the long run. And people being people, it could lead to the greater ostracization of moderate and non-vengeful former CSA citizens. This would make the "morally bankrupt Southerners against the good upstanding Yankees and pioneers" mythology of OTL even bigger and longer lived, leaving some ugly social scars and prejudices among the American public for a far longer time. Regional chauvinism wouldn't be a fringe notion as in OTL, but an accepted part of domestic politics and culture.