This is a fun game, but I think it's stupid to take the story that's presented here seriously at all. If you must consider the story presented in swtor as canon, then I think the best thing to do is to consider it historical fiction written by people in the universe.
Aside from the Heir to the Empire trilogy, the only product of the extended universe that I've ever been able to tolerate was the original KOTOR. It drives me nuts how they seem rabid to trivialize everything that happened in that game. KOTOR 2 started this trend, but TOR takes this and ratchets it up to the 11.
KOTOR wasn't the best in terms of presentation, but it was the only Star Wars videogame to do a passing fair job at it. TOR is nowhere near that level of presentation, partly because it's an MMO. None of us took the story in Galaxies seriously, I advise all of you to similarly ignore the story here and just take it/enjoy it for what it is: a high-grade story for an mmo. "For an mmo" means it's still vastly inferior to what we got in KOTOR. (spread across 8 characters and god knows how much hastily-written backstory - it's still better than any other mmo out there in terms of this).
INB4 digital re-release of KOTOR with improved edited scenes showing Darth Revan & Malak as mere mini-bosses to the sith emperor who is apparently Darth Yoda.
Disgusting.