In a game like Civilization, most of us have launched a war for the purpose of expanding our nation's territory and power, or to weaken a rival nation. In this, we are following Carl von Clausewitz's observation that "War is merely a continuation of politics." In the context of such a game game, and indeed much of human history, such a strategy of conquest was not considered wrong or immoral.
However, the modern world is moving away from Clausewitz's statement. It is moving towards a view that the only moral war, the only just war, is a defensive war. And this is causing an interesting reaction between game players and developers.
Consider the current plot lines in World of Warcraft. Blizzard wants to heat up the simmering conflict between Alliance and Horde. From a gameplay perspective, war is more interesting than peace. It gives players more things to do. To that end, Blizzard has introduced the characters of Garrosh Hellscream and Varian Wrynn, who are pushing the Horde and Alliance towards a war.
However, these two characters are not very popular with WoW players. I believe that the failure of these characters has more to do with the changing nature of war, than by their actual characteristics. If the only just war is a defensive war, then an aggressive leader is necessarily worse than a leader who is mostly peaceful (for example, Thrall).
As well, whichever faction starts the war is the aggressor, and in the wrong. And Blizzard definitely wants to avoid painting one faction as the bad guy. One of the strengths of WoW is that both the Horde and the Alliance have their good points and bad points.
Other games avoid this in a variety of ways. Often one side is clearly labelled as the bad guys, rendering morality moot. For example, in Warhammer Online, the Chaos faction are the bad guys and clear aggressors. Other games have the war between factions being more of an "eternal war", one that has no real beginning and no real end.
But how do you start a war between two good factions, when starting a war is considered wrong? This would be possible in the times when the Clausewitz dictum held, but I think is all but impossible now.