Would it not be possible for a "Treaty" option to pop up, with option_a as accepting peace and seceding provinces, and option_b as continue with the war so players can dictate their own settlements?
It's fully possible in HOI, but I haven't modded EU2 yet so it might be different. However since events simulate the "Fall of Ming" in 1644, which involve a DOW and territorial transfer, I would think that events along such lines are possible.....
What about events that check for French control of certain provinces, and RR increasing/reducing events if key provinces are won or lost at later stages? If revolt risk is high enough and certain provinces are lost, perhaps a "Napoleon abdicates" event can be shoved in, with option a as accept and option b as never, with some stability penalty. Then of course a "Return of Napoleon" event that reinstates him if stability is low after 1815.....and a "Napoleon sent to St Helena" event for late game with the trigger as return of N has happened and money, manpower, and stability are all low? Too bad there doesn't seem to be a way to check for victory or defeat in war (unlike Victoria) otherwise this would be a lot simpler.