After you complete either of the Civil War branches, your commanding officer whether General Tulius or Galmar Stone-First/Ulfric Stormcloak will inform you that you are now free to attack the scattered camps across Skyrim and opposing troops should you come across them whilst travelling however, whilst the camps can be cleared of troops, they will always be present and will never be disabled and attacking the opposing troops that are encountered during random world encounters gets you a bounty despite having permission to do so.