Imperials have traditionally been the race to pick if you weren't sure what you wanted to be, having average stats. This is an ideal position to have a 'beginner' race in an MMO, something with no real weaknesses, but no real strengths either, as such nearly every MMO with races has one (generally as the 'human' race of the game).
This isn't a cliche to throw off, but rather a useful tool to help people get acclimated to the game.
As such it's odd to see that they're going to be unplayable in the game.
So, I'm curious as to why throw 'em out, not for story reasons, but for gameplay ones?
Story-wise, you could probably get away with a handwave about having Imperial Refugees available to one or all of the factions.