Sometimes things need to progress outside the known boundaries because otherwise you can't stimulate the imagination of the players. Again if you can't do that you will stagnate and loose players.
As for new races killing off the rpg cold, I would point out that the wing commander rpg (
http://www.wcrpg.com ) has been going strong for seven years now. It has included several aspects in which you have slated as a no no, such as the introduction of a Kilrathi offshoot faction, the M'Tak'Jor. Also our current campaign 'The Long Cold Winter' features a race known as harvesters, is based from a pervious campaign 'Winter Harvest' which ran about 5 years ago (before WCP came out). 'Winter Harvest' has been largely credited as the best campaign we've ever had and the majority of it was not canon. Even though we've done very little 'canon' work we still have an active member base around 30 with 10 or so regularly attending our weekly sessions.
Summing up my statement I would say that using the Wing Commander Universe as a base while not sticking to canon is fine, as its not so much what you tell, but how you tell it.