<Sigh> Again with the "It was a 9/11 parallel". NuBSG has almost nothing in common with 9/11, less than 4000 people were killed (Not to make light of it, it was a horrific crime, but, doesn't compare to NuBSG annihilation), a drop in the bucket compared to our 6 Billion population.
In NuBSG, less than 100,000, from 12 planets survived to make the Exodus.
After 9/11, Humanity wasn't running for lives and being hunted and exterminated when we slowed down from running top speed. Maybe it was the writer's intent to make that parallel, I don't know, but, I sure don't see the Parallel, there's nothing at all in common other than a difference in Religion.
The Sudan, for one, is a much more apt comparison, and there are many other historical events that are far more apt comparisons.
The 9/11 parallels were deliberate and elaborated upon by Ron Moore--you know, the executive producer and showrunner. I don't know how you can discount his own words about the show's themes unless you think it is entirely a matter of how the individual viewer interprets it--which is a fair position to take. However, it was a deliberate 9/11 allegory on the part of the show's creators. There is no denying that.
Whether the cylons resurrected or not is not the point. If you want to consider yourself on the moral high ground opposing your foe, you don't sink to their level. Barbarism can't be defended ever. There was an interesting moment (one of the very few) later on in the show when a model 6 killed a soldier because the soldier had watched her previous incarnation die slowly. "I didn't do anything to her, why did she do that?" was the cylon's gut reaction. There seemed to be a huge disconnect here between what the cylons as a people did and what individual grunts did. Much like, y'know, human soldiers? The show started off with one unified group trying to get rid of another owing to their dedication to one ideal. By the end it was just a big old mess with everybody being exactly the same. But then they were the same from the start; it just took them far too long to reach that conclusion.
That was certainly one of the show's (clumsily handled) themes: that humanity should not just survive, but be worthy of it, by not abandoning the very things that make them human, such as a sense of ethics, compassion, and morality. What it ended up requiring was for them to recognize that the Cylons were
human, for all intents and purposes. Which meant that trying to wipe them out was just as heinous a crime as what the Cylons had done to the Colonies.
Something the show mentioned on occasion--and a point I think was often lost--is that it's fine to have a strong sense of morality when you have a functioning, stable civilization in which to exercise it. If the occasional person has to die for the greater good, so be it, because you can afford the loss, and the enduring stability of your society trumps that.
But the surviving humans sticking by their principles in the situation presented by BSG? If holding to those principles means your entire race goes extinct, is that really a wise choice? When it came down to it, they did whatever they had to in order to survive, no matter how unseemly it was. Where I think the show erred was the way it framed the issue. When the alternative is the utter destruction of your species, then yes
, you do abandon those principles and do what you must, because those principles will die forever along with your civilization.
There were things Adama said he wouldn't/couldn't do because he couldn't "live with it." Which I'm sure would have been a great comfort when the rest of the human race was extinguished by the Cylons. His personal discomfort with it should have been beside the point, and he should have been smart enough to see that.
To sum up: principles that preserve and stabilize your society are worth keeping; principles that will get your civilization annihilated are not worth keeping. The series was never really willing to have an honest conversation about this. Characters and storylines vacillated back and forth on it, which may be true to life, but makes for lousy narrative.