Try looking up the jedi consular act 3 ending. The two (knight and consular) stories work together explaining why that's possible. I wasn't too thrilled with it either and thought it was cheap, but meh.
I was pissed about the Revan story, too, but I only saw that out of context without the quests leading up to it or reading the book. I'm hoping it's better once I see the full story. Somehow, I doubt it's really over, though. There's patches and expansions to expand on it futher, but the emperor has to go for Palpatine to enter the picture later ... unless he is Palpatine. O.o There's also Malgus's ending which you should look at, too. Do remember, this is Star Wars. Just because someone's body died doesn't mean they're gone forever. Force ghosts and sith spirits will likely be a common sight in the game by the time the first expansion hits.
I just hope we don't get a lot of "____ was merely a setback."