I personally had the same thing happen to me, Rivellon seems to punish thieves pretty harshly, though some countries in the real world do cut off your hand for it so it's considered a heinous crime on earth too.
Anyways when you are taking items that don't belong to you (the cursor is red to let you know it belongs to someone else) you are stealing. They don't want to see you again after you steal from them... How does that not make sense?
They only want to kill you if you steal. If you really just miss clicked it's just a -10 in attitude which does stack up but you must be a real butterfingers if you are miss clicking that many times.
If someone's attitude to you is poor you can raise it by giving them gifts, so "paying a fine" is an option. You can build their attitude back up with money before it dips too low
Lastly your reputation affects their attitude. If they are hostile, doing a lot of good things in the world does increase everyone's attitude towards you, but you have to do a lot of good deeds.
FYI you don't need NPCs to progress on your main quest. There are a lot of places you can access without any contribution from a NPC. Will you lose out experience for not completing their quests? Yes, but then again you chose to piss them off
I agree killing you on sight is harsh, but I'm just pointing out that just because you don't like something doesn't make it stupid. I dislike a few things about this game as well but I realize they are personal preference issues and doesn't think everyone should like what I like to make the game not stupid.
