^ Right, Trent, that's it exactly. You're saying that the Federation failed, because of what is essentially a natural disaster that had nothing whatsoever to do with those ideals in the first place. It's exactly like saying that an asteroid wiping out California makes democracy a silly idea.
For me, I don't consider the Borg to be a "force of nature" or any other such uncontrollable phenomenon usually attributed to them. The Borg are/were controlled by a sentient mind, and in Destiny (and Before Dishonor) they had active intent on killing everyone and everything in the Federation and anyone near. A comet (or hurricane or earthquake) has no such ill-intent and is essentially an accident that such things occur. The Borg were no accident they didn't stumble across the Federation and in the process accidentally destroy billions, they actively made a decision to seek out the Federation specifically and made another decision to actively destroy everything in their path.
But even then, it still doesn't make sense to say that anything about the Borg Invasion invalidates Federation ideals and values. You might as well argue that the Third Reich and the Holocaust somehow mean that liberal democracy and human rights are proven invalid or hollow or whatever. It's nonsense -- if anything, the Borg Invasion (and the Third Reich) proved how important those basic ideals truly are.
And it's important to remember: The Federation stayed true to its ideals. The U.F.P. committed no war crimes, did not violate anybody's civil rights, did not torture prisoners, did not establish a surveillance society, and did not commit any acts of aggressive warfare. And, ultimately, the Federation belief in the importance, morality, and utility of multiculturalism was what convinced the Caeliar to renounce their xenophobia and isolationism, disband the Collective, and accept its liberated drones. Federation values really did save the day.