Short answer is that while they are licensed to use the setting, the franchise still belongs to Lucasfilm and a certain amount of emphasis is placed on not contradicting other sources where avoidable.
And, they could do that pretty easily by declaring the game to be set in its own time line which may, or may not, actually lead into the stuff that comes later. But, if it's LucasArts refusing to loosen the reins that's the issue, then I suppose there's nothing that can be done about it.
From a story-telling perspective (especially in something like an MMORPG) it seems horribly limiting, though. Kind of makes you wonder why anyone else would even want
to try to write a story in the Star Wars universe.
Oh well... I'll still be using the alternate time-line thing as my own personal Canon, for now, at least. Pretty sure Lucasfilm can't actually come after me for changing their story in my own head.