Instead of extinguishing war, the Federation has applied it to new frontiers. We might not fight among our fellow humans, and we might not militarily impose ourselves on new societies, but we are not going to sit around and be conquered by an aggressive alien opponent.
The original series: Cold War
In Star Trek stories, We Come In Peace. But peace and compromise go only so far, and even the Federation's "evolved sensibilities" aren’t going to give in to an adversary encroaching on certain rights.
War is not pleasant, but nor is it "bad"; it’s a morally neutral act that can be employed for good or evil purposes. We can easily argue that there are good reasons to go to war -- stopping Nazi Germany in World War II is an obvious example. Disputes over territory, differences in ideology. Righteous protests against abusive authority.
Trek is aware of this and does not pretend to be "above" war.
Perhaps the earliest evidence that conventional warfare survives into the Federation era came with the original series episode "Balance of Terror", in which Kirk engaged a Romulan enemy in submarine-like games. This wasn’t actual warfare between two governments, but it did show a battle in a cold war (the episode first aired in 1966) between to opposing sides that had once fought openly.
Later we’re introduced to the Klingons, another former war enemy who become a standing symbol of the real-life U.S.-Soviet Union Cold War relationship until Star Trek VI: The Undiscovered Country tied up the storyline with a treaty.
The Klingons, in fact, were introduced in "Errand of Mercy" -- an episode, interestingly enough, in which Kirk vehemently tries to convince a society of pacifists to rise up and engage in war because their rights were being trampled.
Otherwise, the Cold War-era model would remain the standard in Trek for decades to come. Writers could tell action-oriented stories of isolated skirmishes and proxy battles, but references to actual sustained warfare are rare.
The Next Generation’s most notable war stories were probably "Yesterday’s Enterprise" (imaginary war: the story of a Federation-Klingon conflict that took place in an alternate timeline) and "The Wounded" (war after the fact: O'Brien and his former commanding officer struggle with the memory of seeing Cardassians massacre a defenseless population).
War engaged
It’s not until we get to the latter stages of Deep Space Nine that the franchise seriously tackles issues of sustained warfare. The Dominion War storyline is a very important one because it showed that although Trek has always tried to depict a positive, moral view of future humanity, war is something we’re not likely to simply and easily escape.
I’ve long maintained that Trek's positive outlook is only strengthened by the possibility that things can turn bad and that morals are not absolute. By putting the very core of the Federation to the test, the writers were also testing the franchise's highly touted "positive outlook" and "Roddenberry values."
Storylines crucial to the war storyline like the tour de force "In the Pale Moonlight" showed that Sisko and Starfleet were willing to put certain ethical issues aside -- resorting to lying, cover-ups, bribery, and even looking the other way during an assassination -- in the interests of survival.
DS9’s war storyline provided not only an ongoing backdrop for the series, but also a new spin on the nature of the Federation. When an unofficial covert spy organization -- Section 31 -- reared its head in "Inquisition" and to an even greater extent in "Inter Arma Enim Silent Leges," we learned that perhaps the 24th century contains those out there who are willing to break the rules so that we might survive to live by them. Again, ethics give way to survival.
The beauty of such arguments was that they showed the world as gray, and not as a place where overriding proclamations of "correct" ethical outlooks -- Roddenberry-esque or not -- were necessarily in our ultimate best interests.
Aside from ethical situations, sustained warfare on DS9 also allowed the creators to explore situations atypical for Trek.
In "The Siege of AR-558," a battalion of Starfleet soldiers (is that normally an oxymoron?) are seriously battle-fatigued. They’ve been to an ugly place few humans in the Trek universe have been. And until anyone has been there, how can we know whether a Starfleet officer with that "evolved sensibility" wouldn’t crack under pressure and become violent and dangerous? "AR-558" suggests that our tendency to turn to violence in the interests of survival is not something we can simply detach from our psyche -- or evolve beyond. And for that matter, we may not want to.
The meaning of future history
So what was the Dominion War really about? A clash of ideologies? Territorial disputes?
Ironically, the war -- as outlined by the writers -- was actually built on that old foundation of "good versus evil." In the broadest sense, the Dominion were simple aggressors, attempting to conquer humanity and the Alpha Quadrant merely so they could better control it.
It’s only two seasons after the writers start the war that the ethical issues arise and become interesting. In that sense, the war existed so the writers could feed the show more drama, with a military flavor. Like many things in Trek, it’s mostly its own dramatic little monster.
Beyond television, of course, warfare is deadly and destructive. It solves problems, but only by silencing opposing arguments with death. Simple logic (Vulcans are pacifists) suggests that it’s best to avoid war if peace can be achieved. But in a world where ideologies clash and groups cannot come to terms with differences of opinion, rights, or territorial claim, there’s probably no avoiding it -- eventually.
The fact that Federation have put aside all such differences to achieve perpetual peace among humans is a miracle -- or more likely another of those fantasies that allows Trek to be what it is.
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