I think the Emperor's death would destroy the Empire. The Dark Council would squabble over who should be Emperor, leading to a battle between all of them. The Sith have always fallen apart without a strong leader, and start killing each other to get a chance to rule, hence the Rule of Two. Unless Marr puts the entire Council in its place, the Dark Council is going to be destroyed. Which pretty much beheads the Empire.
TBH I'd rather see is focused on just one class. Once you get all the classes involved its gets complicated (these guys can't meet remember) makes the story repetitive and removes the possibility of other class stories. Also is would be a bit weird concerning the Smuggler and the Bounty Hunter. Yes, nobody want's the galaxy to be destroyed - but it just doesn't fit with the 'mood' if you like of their story.
And yeah, out of game is the best. I think in-game it would be cool if the Sith Warrior had to collect all the pieces of the Emperor together to restore him back to life or something... or any SE quest focused on the Emperor. Or, maybe the SW collects his pieces, but learns of his mad plans to destroy the galaxy. And then theres a light side dark side choice at the end deciding whether to keep him alive (in return for great power) or destroy him.
But then, concerning a novel, it may mean giving the 'heroes' canon identities - which would anger a lot of people. And kinda of irk me personally. So who, other than the heroes could destroy the Emperor? Maybe it is best to leave it to one in-game class quest...
But then who would replace him? Maybe the Dark Council could make the Emperor a sort of myth and keep everyone believing, while Darth Marr leads from the helm instead.
I don't know, but it will be interesting to see how it all ends. I wasn't there to see how Galaxies ended (though I would probably end up back on my moisture farm like the good Uncle Owen I am ), so I intend to stick around for the finale.