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One of the reasons why I'm profoundly grateful DS9 was produced in the 1990s, as opposed of today, is that today, we'd never get Kira Nerys as we know her as a main character, nor the ambiguity in the presentation of the whole terrorism/freedom fighter issue.
Now of course one might say that the label "terrorist" is purely Cardassian propaganda, i.e. a misnomer by the show's certified villains which the viewer is not expected to take seriously. (Though I bet that in a hypothetical DS9 produced today, even the villains wouldn't use the expression.) However, Kira calls herself a terrorist quite freely and repeatedly (an example that comes to mind would be her arguments with Thomas Riker in season 3's The Maquis), and there are enough episodes on the show to demonstrate that the popular conception "freedom fighter = heroic guerrilla soldier who only ever kills members of brutal occupying force" and "terrorist = ideology-driven bastard who might claim lofty goals but kills civilians galore" does not work here. And Kira and the Bajoran Resistance during the Cardassian occupation weren't the only arguable case; the show's heroes themselves could not agree on whether or not the Maquis were terrorists. Was Dukat a terrorist when he fought against the Klingons by his lonesome Bird of Prey armed self between Return to Grace and By Purgatory's Fire; or when he turned into the Emissary of the Pagh Wraiths post-Waltz? What about Damar and his resistance, which as Kira points out has to be willing to kill their own people in order to win against the Dominion?
A terrorist is a terrorist is a terrorist, to misquote Gertrude Stein. Except, one might add cynically, when he wins, in which case he's a successful freedom fighter. To put it less glib: obviously the Bajoran Resistance in general and Kira in particular had a very limited set of choices. They were fighting against an occupying force that was vastly superior as far as weapons were concerned, and which was brutalizing and exploiting their people. So they used their bombs to cause the maximum damage without having the chance to be discriminatory about whether or not they hit people aside from the Guls they were intended for. And if some of these were civilians - (think Rugal's mother, mentioned in Cardassians, season 2, or Siluren, assorted other servants and the family of the Gul in question, mentioned in Between Darkness and the Light, season 5) - then that was the fault of the occupying force because they shouldn't have been on Bajor to begin with. Case closed.
Except this rationale, if you think about, sounds not to different from what some Iraquis right now might say. Or for that matter some Palestinians. Kira, as represented on DS9, never stops believing that what she did was necessary to free her people, but she never kids herself that it was always morally right, either. When Dax asks her, in season 2's Blood Oath, "How many people did you kill?", Kira replies "Too many", and her expression makes it clear she does not think back on this with a feeling of triumph and complete justification. Nor is she characterized as being completely "above" the mentality that dispenses lethal and none too discriminatory judgements. In extreme circumstances - as in her encounter with Siluren, or when being confronted with her mother's affair with and affection for Dukat - she can still say "you all deserved it!" (to Siluren) or a cool "what about her?" (thereby agreeing to kill her mother together with Dukat, something Kira Nerys only changes her mind about when listening to her father's message for her mother, not because Kira Meru has done nothing to deserve being blown up but sleeping with Dukat). Which makes psychological sense. Coming to terms with her past, being able to see behind the façade of Marritza in Duet or to forgive Tekeny Ghemor in Blood and Water is an ongoing struggle for Kira, and it includes dealing with the mentality that helped her survive and contribute to winning the fight to free Bajor. Which is both a freedom fighter and a terrorist mentality. I don't think any main character of a show produced post-9/11 would be characterized in such terms; after all, if Kira is sympathetic and admirable, what would that say about the foes in the war against terror?
Given that the Cardassian Occupation of Bajor is strongly coded to resemble the Third Reich, one might argue that here lies the answer; DS9 implies terrorism is a tool that can be used against a fascist and/or genocidal state (see also: The Dominion) only. But then what about the Maquis? In his first open conversation with Sisko at the end of For the Cause, Eddington bitingly compares the Federation with the Borg and tells Sisko that the reason why the Maquis gets vilified is because the Federation can't deal with the implications of its existence - that in a supposedly perfect democratic society, individuals would still found an armed organization against their own government.
As opposed to the acts of the Bajoran Resistance, which form the DS9 backstory but are only rarely seen, via flashback, we don't hear too much about civilian casualties of the Maquis, which forms part of the ongoing narrative of the show. (Perhaps because of the then simultaneously running Voyager?) One of the crucial events of the entire Maquis saga, though, is Eddington using biological weapons to make an entire planet uninhabitable for Cardassians. Which is responded to by Sisko using biological weapons to make another planet entirely uninhabitable for humans (and Bajorans, one presumes). Both acts undoubtedly qualify as terrorism in the sense that we use the word. Other Maquis acts as presented on the show include kidnapping and the acquisition of WMDs. The primary justification the Maquis bring up is the fact that the first treaty between Cardassia and the Federation (see also: TNG's The Wounded) consigned several of their planets to the Cardassian territory (just as several Cardassian planets ended up in Federation territory). Jewish settlers or Palestinians? Draw your parallel of choice. One unintended by the writers, I guess, but in a world more alert to the ever increasing violence following ever increasing rethoric, it could be drawn. The way the Maquis plot thread ends isn't exactly comforting for either case; the DS9 writers saw no other way out than heroic suicide by Eddington, who became that particular threads main representative, which leaves the essential argument between him and Sisko as the representative of the democratic status quo unsolved.
Of course, by that point of the show the Maquis sub plot had to be wrapped up, as the big final war arc was to begin, and Sisko himself was about to go guerrillo on more than one occasion, but that's another chapter. There is one other thought, though, in regards to the presentation of terrorism on DS9; more often than not, those terrorists have strong religious beliefs. The Bajoran Resistance, obviously, by and large never lost faith in the Prophets; Kira certainly never did. While the Cardassian Occupation put an end to the old Bajoran caste system, the essentially theocratic nature of the Bajoran government remained unchanged. The Cardassians, otoh, season 7 Dukat and his Pagh Wraiths aside (who also qualifies as a terrorist, btw), are presented as committed to an ideology of service to the state but not to a religious belief. This makes for an interesting reversal at the end of the Dominion War, when the irreligious Cardassians are the resistance (terrorists?), and the strongly religious Dominion the occupying force, but then the Dominion brand of religion, enforced through genetic modification as it is, never gets presented as positive to begin with. Suddenly I have a vision of a post 9/11 DS9 which starts with Sisko arriving and telling the Bajorans that they can't possibly become members of the Federation, or indeed masters of their own planet now the evil tyrant is gone, before they don't become a democracy, but that becoming a democracy by no means should entail handing over power to the Mullahs Vedeks… and I'm more glad than ever that the show was made in the last century.