Far Harbor is so far beyond the writing of Fallout 3 and 4 I seriously wondered if they found some New Vegas guys to ghostwrite it. There are no good answers for how to resolve DiMA's situation, just what you can live with. They even put a human face on the Children of Atom, which until Far Harbor functioned on the level of a cartoon.
I guess because they wanted to show that all the factions are flawed but arent necessarily evil per say.
The people of far harbor are honest and mostly innocent but they do show they can be quite needlessly aggressive with mainlanders (but you can build their trust, like your choices suddenly matter now or something) and can jump VERY quickly into the murdering part (they dont even consider the possibility to give their prisioners some sort of trial beforehand to give them a chance to explain themselves, its just what they see and thats it).
The children of atom can come off as a crazy cult (and ultimately thats what they are) but interact with them enough and they come off as misguided by their leaders, especially since we know the cult didnt start off violent and it mostly focused on good values like being kind to your neighbor, forgive their sins and etc (hell a good way to get good karma in F3 was donating to them) and they never turn violent on you (unless you shoot first obviously). Hell, you see some of their own members showing concern towards their fellow members, some you can see are just sad victims of this world in despered need of guidance and help (like one of them being a jet junkie). It shows the leadership is their true problem ultimately and the children of atom can actually return to being a harmless influence.
Acadia is a safe haven for synths who understandably dont get themselves involved much with the railroad (they find the whole mind wiping and then hiding thing to be rather...wrong and burying the problem, as if the only way a synth can be "free" is by pretending to be a human for the rest of their lives, even if they are unaware. We did see how this can backfire in Fallout 3 with The Replicant Man questline, it ended alright there but it seriously could have not). However, its peace is built on lies, which raises the moral questions if this means they are no better than the Institute and Railroad and if they all should suffer for the actions of their leader.
There is no "evil" faction in Far Harbor, even the Children of Atom turn out to simply wanting their own version of the greater good and you can even make the argument that a change in leadership and Far Harbor's extreme treatement of outsiders is what is truly the root of their problem.
There is no "perfect" ending, you can just pick your own version of "peace/justice" and come to terms with it as you now know your morals have been questioned if not outright deconstructed.
Its almost like Far Harbor is mocking the lack of moral ambiguity in the base game, even if unintentionally. Turns out your 4 little options that are usually variation of the same answer wont give you an easy answer...