I honestly think Star Trek VI provides a pretty good frame for this thread. A good chunk of the plot was about whether or not the mighty Klingon Empire would be ready for peace with the Federation -- because that could signal the end of Klingon tradition. That's very much hegemonic fear that faces modern-day globalization, and the thing that Eddington really meant.
Now, am I siding with Chang and his fellow conspirators? Or Eddington and Co.? Of course not. But I think a valid point was hit upon by Azetbhur: if the Federation is so welcoming of a variety of aliens, why is it primarily run by humans? Why is everything up to human standards? Who SETS the standard, and why must everyone be subjected to, again, "inalienable human rights?" Is that idea not hypocritical to IDIC, That in the vastness of space, the morals of humanity are the morals the rest of the galaxy should follow?
That's not the outright tone in much of Trek, but you have to admit, whenever there's a spark of violence between two alien cultures and our heroes have to intervene, it's always through human ingenuity or trickery or solution. Whenever there's a mysterious, powerful alien entity out there, it's always Human Nature that ends up satisfying the creature or letting our heroes evade certain death. Humanity always comes out, humanity is supreme, and if you don't join us, well tough luck, you're not getting into Perfection. To me, that's a valid point that helps the "Federation = Borg" argument. Heck, even TNG/DS9/VOY Earth was basically Eden with flying shuttles. That's much prettier than what the Borg have, but to the Borg, a hive-mind IS Eden, so in essence, there's no difference there. Join Paradise, or else.
However, whatever these arguments are, there's always a proper way to bring them to the table. Eddington's way of reverse-psychology and guerilla tactics of realistically unmitigated violence is a big no no. Chang's assassination squad is a no no. Yet Ahzetbur, the one who brought up some of the most damning charges in the movie, is the one who truly does lead her people to peace with the Federation. Someone like Chakotay, who hated the Federation to the core, ultimately came to embrace it because he got to see the good people that it bore. So then, to me, it seems that the perfect counter to the whole "Federation = Borg" argument is that the Federation leads by example.
(that being said, forget the whole "Destroy whole fleets" aspect of the Borg analogy. For one thing, Eddington was clearly talking metaphorically, not literally. In no way was he ever comparing Borg advancements in space and technology or any other such silly thing. The whole Sisko Vs. Eddington arc focused on ideology, not just capability. Any argument saying, "Well, the Feds never built a huge-ass Cube!" conveniently forgets the context)
Ultimately, it comes down to differences of opinion (that whole pesky IDIC again. If your radical ideas are shot down, is there true tolerance in a society?). I would think that in some regard that Eddington won a lot of points when he faced off against Sisko. Not because of the Fed/Borg analogy, but because he provoked discussion, which is what a political minority tries to do. A lot of the villains in DS9 were never meant to be black-and-white mustache-twirling types, and Eddington is no different, but the fact that there's discussion about the nature of the Federation both within Trek and outside, I'd have to say that he achieved one of his goals: raising awareness of a problem (albeit in tragically misguided ways).
