Can two or more sides be 'fighting the good fight' against each other? Of course.
In one of the novels I'm currently working on, the main political storyline revolves around a plot that sees several great houses of one nation fighting each other for control of their nation's crown after the royal family is apparently assassinated. Each house has basically equal claims to the throne, each house has what they believe are valid reasons to oppose the other houses' claims, and each is fighting to keep the nation from being ruined/over run by outside influence.
To top it off, the surviving prince of the 'dead' royal family returns at the head of an army from another nation, believing he is leading the last of those who would loyally support his family's claims against usurpers. He plans to marry into the royal family of the other nation, and join the two into a greater empire, after he kills those who betrayed him and brought war to his homeland.
Lastly in the plot there is the beautiful twist that the entire war was drummed up by a religious leader in the second nation who was attempting to draw even more nations into a holy war/crusade so that his homeland could rebel and strengthen their position while most of the armies were abroad.
Every party is acting in the name of good. The houses are fighting against corruption, dishonour, betrayal, etc. The second nation is fighting against tyrants and heretics. The other nations that would march to the aid of the first nation are doing the same. And the entire plot was designed to overthrow an oppressive empire.