Its not part of a quest. When i travel form A to B i never fast travel. When i see a stormcload camp, im going there to kill them.. But ive noticed that there are Stormcloak members who cant be killed somehow.
Its an issue with the fact the game doesn't unflag them as essential when you join the Legion. Legion/Stormcloak quests mirror each other, so those guys are basically the same as the quest givers at the Legion camps.
It shouldn't be an issue, you can just leave the area once you're done. But except for the use of console commands, you're not going to kill them.