Talking about griefing is a hard subject, especially when there's no testing. It's kind of like talking about a car that's being built and people predicting that the brakes are going to fail. You can't really have a good, thoughtful discussion without test driving it or watching someone test drive it first and all you're left with is assumptions, predictions, and general opinions about the car.
My thought is this:
People are going to figure out ways to mess with games, developers know this and they try to prevent it as much as possible. Like those games, it will probably happen in COE but I can say with certainty that SbS has a good collaborative mind and can work to mitigate these problems as much as possible. However, it's also on US as players, as testers, and as community members to report these issues and not let them go unreported.
Your example isn't bad per-say, it's just that it's hard to discuss without anything physical. First we would have to believe that this is the mechanic in place (that NPCs run away from people who have a weapon or fists up) and then we'd have to believe that there's no way/fix around it without having complicated laws that are hard to follow.
In regards to your example, I don't personally believe that NPCs would be created to be that skittish. In a perfect world, I could see most NPCs (depending on their profession, etc) mentioning the fact that a player is in a combat stance and that it's a problem to them, but not interrupting whatever it is that they're doing. Kind of like how in some games, if you are holding your weapon and try to talk to a NPC they will say "Heck no, I'm not talking to you until you put that weapon down.". As others said (in other ways), if you had a knife out in a store IRL there would be some consequences. I don't see why that can't happen in Elyria too, maybe NPCs will remember that the next time you try to buy something and go like "hey, that person was super threatening in town...they make me nervous and I don't think I'll sell to them without talking to them more" etc etc. Again, this is all opinion...I think the planned Reputation/Communication Systems will also greatly help in preventing extremely overt "griefing" (aka. actions taken by players that give them no direct in-game benefit).