I wont argue about game code and dev's intentions. But I would like to point out that Broken HIlls is set to explode, from the outsiders' storyfag's point of view.
The destruction of the mine purifiers beforehand by the humans (that we got the quest to fix it). This affect mutants lightly because they can stand the damaging air quite well. So from both side it look like a dangerous and expensive prank, but not deadly.
The Massacre: the fact that Marcus set out to arrest Jacob for that crime, since we hide the note from him... that fact is guaranteed to explode that powder keg. The humans know that their side dont do it, and corpses got the signs of being cut down by heavy weapon ("chewed up"). The mutants know quite likely their side do it, what with the corpse' signs, and the disappearance of Francis.
It's like one side poke and the other smash back with a hammer.
It's inevitable because we dont have a way to make Francis not massacre those people.
And yes, I do mean the mutants brought that bad ending.