This whole KOTOR storyline should have been concluded in a KOTOR 3 game and SWTOR could be a fresh, new start. Honestly I don't like the fact that I forced to kill Revan and HK-47 (twice!!!!), the iconic figures of the previous games. And I don't like the fact that my KOTOR2 character was simply killed outside of the game in a "novel" (which is more like a draft script than a novel) and I can see her as a ghost in a flashpoint.
Sure, from MMO perspective these are epic moments. From KOTOR perspective I think these are poorly executed stories.
Look at it this way regarding Revan: You struck him down and he'll come back in a form more powerful than you can possibly imagine.
And for HK-47, well, he was seen running around on Mustafar during the time of the Rebel Alliance, so he's not exactly killable in this era.
I think Revan (the novel) should have been KOTOR III not the other way around (and I think it did more harm than good to the KOTOR gamer, but it is what it is).
I do think Revan will make a return after the foundry, but I hope it's not exclusively in some sort of "Red vs. Blue" rivalry with the Sith Emperor - he should have more to contribute to following arcs than just that.