Do members of a faction that are innocent of any supposed crimes still worthy of the same "punishment" as the rest? Its a question that is up to the individual to decide.
Completely and fully, in my book. They reap the benefits of the atrocities their nation/state commits, they get to burn with the rest when someone finally steps up to take them down. With the Enclave and Legion, it's not even a moral dilemma. The Wanderer/Courier is simply returning unto his/her enemies as they have done to others, so it's nothing more than a balancing of the scales. Neither of the aforementioned powers would show mercy to the civilians and families of those they slaughter, so their people deserve the same amount of mercy in return.
Yes, I realize fully what that means in real life. Warfare is
shitty like that. In the end, see my sig line. It's the way the world works. Wars are ultimately won by being willing and able to be more brutal and calculated than your enemies. The idea of a so-called "clean war" is a asinine idea born of the 20th century, despite the emptied and charred ruins of Europe and Japan after WWII being a mute rebuttal of the whole line of thought. Your enemies will never cede anything to your "victory" unless they've been smashed down to the bedrock and forced to do so with a boot between the shoulder blades.
Attempting to apply morality to warfare, the single greatest immoral act humanity can perpetuate on itself, is not only a lost cause, but serves only to reinforce and allow other crimes and atrocities to be committed without consequences due to fear of war by those powerful enough to step in. Ultimately, on the large scale, might makes right. Because if ones entire nation and people have been blasted back to the stone age and forced to rely on their enemies to survive and rebuild at the cost of whatever culture they may have had, than they don't get to write the history books.
In FNV, it's why I don't even consider the Legion worthy of human rights. They forfeited them when they decided to try their hand at expanding their idiotic, worthless, dead end and meaningless so-called culture at the expense of their betters. Their reward for doing so is total contempt and destruction at the hands of said betters. They are worth nothing, are worthy of nothing, and will be left with nothing before being burned to ash and tossed into the dustbin of forgotten memory, never again to trouble the minds of lives of those better than they.
Because that's how humanity works. There is no morality, there is only power and the ability to force others to bow to it. Everything else is sugar coating and sheep herding.