It's understandable that some people find the alternative bad endings upsetting since it suggest some quite horrific events. If it was just "lights out" it's one thing, I can buy that, but developers have since the beginning of the game suggested that some of them will face the worst of the worst if you allow that. And you can't prevent it since they now also decided that you can't be on the good side with everyone of them. Meaning that the whole premise of the story contradicts itself since you were suppose to change the outcome.
Like others have said, the world is already a bad place, perhaps don't include that in a game that honestly is quite romantic at times if you look deep enough. I can't recall what's been said officially, but I think the truly bad endings will be optional. Otherwise if forced you would alienate a large majority of people interested in the game since most of us aren't interested in... that stuff.