Oh boy . . . the canon discussion again. Let me take a crack at this even though it's late over here right now. Let's try looking at this from a different viewpoint. Prepare for a wall of text.
a) The game is released in 2004. It was created by Obsidian which according to many reports didn't have the time to give the game the final polish it apparently needed before release. They were denied to opportunity to do a content patch which pretty hosed their attempts to fix the plot issues and many of the bugs that were there on release. Yes, there were official patches but those were mostly minor bug-fixes. Hopefully we can all agree at least on this much.
The formation of canon: Many of the those on the canon bandwagon like to site the "Knights of Old Republic Campaign Guide" that came out in 2008 as the be-all and end-all as the canon source. It's a nice book. I own it.
But made the authors of this book the arbiters of canon-hood.? Chris Avellone (with Ferret Baudoin) wrote Knights of the Old Republic II. The authors of this book were Rodney Thompson, Sterling Hershey, John Jackson Miller, and Abel G. Peña. I would think that canon would come from the authors of the game not from the authors of the book. But you cry out: Lucas authorized the sale of the book? I'm getting to that argument presently. We can also agree that it doesn't quite get everything right either. It states that the Handmaiden was supposed to accompany the Exile on her journey. You trying doing that in an un-modded game.
c) SWTOR Canon: Meetra Surik is what they call the Exile in the "The Old Republic" game which came out last year. (I'll not debate the merits or disappointments of that game here as this is a TSL thread. There are other threads here on this site for that already.) That game too is an official product. Well, there's all this stuff in the game about that character and none of that was written by Chris Avellone. Doesn't that make it not canon? Before anyone pounces on me for being a TOR hater, I own that too. . .
d) Continuing on canon: According to Desmond's definition of canon, it could be argued that the entire un-modded game of TSL as-is deviates from the established canon of the first game. Let's be honest here: there was a lot of retroactive tinkering with the Revan character in TSL. I'd argue this but I think that Scorchy explained that very eloquently in his walkthrough of TSL. It's a very long read but well worth the time.
e) There's also debate on what "Star Wars canon" is as well. Have you ever seen the Wikipedia page on it? It's a product of a maddened mind. The general gist of seems to to boil down to "only the Star Wars feature films are canon." Who is to say your concept of canon is superior to anyone else's.
Desmond, you didn't start this off by asking if it's canon but you continued the conversation on it so I'm directing this at you. Which canon? What is your own defintion of canon? There's too many variables here at work for any project - even if it was released by LucasArts - for it to fall into all areas of canon. It's impossible. Instead of this thread getting derailed further - and making me split the thread into an excruciating discussion on canon and the original line of thinking - I make you a proposal. Play TSL through according to your nebulous definition of canon and then try out the mod.
And finally: Just remember . . . it's just a game.