Nah you are right about the themeing. I take it as saying that the Republicans and the Separatists so suddenly found themselves fighting the same enemy. All the reasons the Seppies hated the Republic remain, and all the affection the citizens of Ferrix have for their republic have been taken away. The clones within a moment became stormtroopers, which plays into why the CIS was fighting them (on an individual level) and how the Republic's good had become so easily excised.