A mistake common to virtually all Game Masters is the sense of trying to balance the story as the players go up in levels and become stronger and more formidable. When it comes to roleplaying it is often the players that make this challenge worse. More times than I can count (and I am guilty of this when I first started playing, too) players refuse to accept that just because it is a game doesn’t mean that all cultural and societal norms get tossed out the window. If a zero-level King tells you to go kill a troll, then the 4th level warrior goes to kill the troll. Just because you can in theory smash your way to the top of the chain of command doesn’t mean you can without any consequences.
This is important for players and game masters to accept. A 20th level wizard might easily seize power from a low level NPC baron, wiping out all of his armies with a single spell. But just because an NPC is a zero level warrior or even a 3rd level rogue doesn’t mean their life is without merit. Kill enough low level NPCs and somebody is bound to take notice. Maybe it is a powerful villain, monster, or divine wrath but something akin to karma is going to catch up to the player that abuses their power. As a cautionary warning to any players seeking to flex their muscles; unknown powers have muscles too.
On the bright side, and this is by all means a bright side, the players should consider themselves to be the elite of the elite. A good game master will encourage this feeling of being proper heroes. And proper heroes don’t abuse their power. That kind of thing is better left to the suspiciously evil Archbishop and his henchmen. Figuratively speaking, of course. The Archbishop hasn’t actually done anything to hurt anyone, right?