You don't kill the Emperor. And both sides have to fight Malgus.
Edit: SW kills his master, and his masters master (Not sure if that is a Dark Council member or not) but no republic people. SI kills a Dark Council member, but again no republic people.
Empire stories are all more about consolidating the players power than fighting the republic, while the republic stories are about defeating the empire in some way (Not sure about Smuggler or BH though because I am playing BH and have avoided spoilers, and I couldn't give a rats *** about the Smuggler