Right, it is stuck in combat mode even if there seems to be nothing around, or it is just a glitch.
You can try a console command, putting the focus on the NPC in question by clicking on it when the console window is open. You will see the name of the NPC at the top of the screen. Any way, the command is
stopcombat
http://fallout.wikia.com/wiki/Console#NPC_manipulation
In the future, have a series of saves for about every half hour or hour, along with the ones you cycle through, like a milestone save before you take on a series of quests, or at stages along the way. Sometimes you will want or need to go back about two or three hours to fix a bad glitch or from picking the wrong branch.