Any Confederate guerilla war - especially after Appomatox or its equivalent - will quickly degenerate into mere banditry and will be handled as such except that the cops will have the support of the Union army. The lack of any kind of logistical support for a long term war dooms it. The area most beneficial to a guerilla war - the Appalachias - is actually a hotbed of unionism.
Any large sized guerilla bands will probably be defeated before end of 1866, breaking up the units into smaller and smaller bands. I say after a few years of increasingly futile and ineffective banditry, the guerillas simply give up and go home. Because of the ongoing fight, Andrew Johnson won't even argue with the Radical Republicans and impose a more comprehensive reconstruction.