The most annoying thing about how Bethesda does their essentials, is they fucking half ass it.
They'll make a couple people essential in a faction, the rest (some of which include important quest givers for location side quests, debatably more important than the essential ones) are free game.
So you end up with the locations breaking in terms of quests, ruining any point of going there, but annoying twats will remain there forever.
It's like you can make entire locations into limbo-zones, it's bizzare.
For example, you can massacre everyone in the Vault 81, of course, no one gives a shit, they'll forgive you in a day. But the "Hole in the wall" quest will never start, because Bethesda couldn't just make ONE more character essential.
They seriously need to just go complete Stalker and make 'safe zones' where you can't draw weapons, or just go full morrowind and go 'fuck it, kill everyone, enjoy'.