It's an open world game, if the devs think punching random people is "playing the game wrong", they're making the wrong genre. In any open world game, the players will try to attack and run over absolutely everything.

Also they had eight years to come up with some kind of a consequence for killing important characters. They could just do something like EVE Online does with "cops" in high-security systems - it wouldn't make as much sense since this isn't an MMO but it would still be better than invulnerable characters and characters surrounded by invisible barrier so you can't even knock them over with a car. That's just shit.