A little re-examination of my thoughts before might be in order. Thanks for the alternate viewpoint!
I agree with you that it was important to show that such an optimistic outlook can work, at least within that universe. Thus the Dominion War becomes analogous to the "surprising" successes of the democracies in World War I, where a way of life that seems inferior or naive to the traditionalists of the day proves able to hold its own.
I would caution future Trek writers against emphasizing the darker sides of characters and their morality, however. The important philosophical point here is that Trek characters sticking with their "more evolved sensibility" is a better way than stooping to amoral (or outright immoral) acts to "preserve the Federation at all costs".
So I would say that reaffirmative/redemptive conflicts like the Dominion War are important, both to history and to affirm the Federation's principles. It is not, in my opinion, okay to have the characters compromise those principles! That directly undercuts the philosophy.
(By the way, I think that any future series should focus on the ouster and dissolution of Section 31
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