yeah, but the soldiers are called "Sith Soldiers" and their leader was the "Dark lord of the Sith". wouldnt it make sence that if your on the dark side, you kill the republic?
Well, I suppose that is the "mater plan". The sith are stronger now, so if you get control from them, then the republic is just a bump in the road.
I think the sith lords will be like the star forges from the first game, you kill them to advance the story. Each planet has a sith lord. So the troops their would be loyal to their respective lord.
Besides, in the first game, Malak was the uber-sith. So why would you turn against the only advantage, the republic, you have on malak?