I'd honestly say that the matter of conformity in pursuit of an ultimate good isn't necessarily a bad thing, and it is probably not strictly correct – at least from a utilitarian standpoint – to simply say that it's wrong to expunge extraordinarily dangerous threats because it may trample freedoms along the way seems rather black-and-white and unrealistic to me. I'd say that adding the additional qualities of imperfection to the Naaru and emphasizing the potential danger of becoming too embroiled in the collectivist mindset is hugely dangerous, especially if you don't know what you're doing entirely (see: the Scarlet Crusade, who weren't exactly enacting the will of the Light, just projecting their own interests over it) is plenty good, but that trying to make the Light into another shade of gray feels awkward when it is by definition what anything "good" is. Philosophically, it seems to elevate personal choice over all other things, which feels incomplete and absolutist.
I think that one important part to why it should be a conflict isn't just that they need to keep one another in check—realistically, if we're looking at it from a Hegelian perspective, it will actually only help elevate every force, since the ensuing sublations will allow the forces to overcome their inherent flaws. Looking at an example from the actual lore, Disorder was made more effective and powerful as a force because it took qualities from Order—that is to say, a Titan conquered it and made it an organized army. The Void and Light regularly take physical qualities of one another with the darkening of Naaru, and this advances the interests of both—the Void extends its corruption, but the Light can often make something good out of it (see: K'ara and M'uru both).
The idea of a massive Cosmic War is interesting, so long as it isn't summarized into a single expansion and is allowed to be an underlying factor controlling the plot from hereon out.