Does that mean that the series bible for WCA was invalidated by the movie?
The behind-the-screens material isn't ever really "canon" unless it's published. I think you'll find, though, that that Academy series bible is largely invalidated by Academy itself. It was written at the start of the project when the idea was that the show would use all the Wing Commander III characters instead of new ones. Check out the character bios--you have Flint instead of Archer, Hobbes instead of Gharal, Cobra instead of Payback, Hyena is Vagabond's brother and so on (and Kilrathi characters based on the WC3 aces, that would have been cool!).
Another thing: If you needed a pilgrim to navigate (before the navcom was invented) how was trade possible? The confed spreads out to hundreds or thousands of worlds and systems. There must be millions or billions of trade ships and convoys and personal transporters.
So there was always a pilgrim on board of every human ship? How numerous was this "minority"?
The movie itself doesn't say, so this is outside of that particular line of criticism, but the Confederation Handbook gives a detailed history of it all--which I will try to sum up here as best I can.
I suppose you first need to know that 'Pilgrim' means multiple things. The best analogy I can think of, if you can forgive it, would be saying that someone is a 'Nazi' during World War II. I might be referring to a person who happens to live in Germany while it is an enemy state, someone who follows Hitler's ideology regardless of where he is or someone who is actually a formal member of the Nazi party.
Similarly Pilgrim can mean someone who has the 'jump mapping' ability (a "Savant"), someone who follows a specific religion (a "McDanielite", followers of Ivar Chu McDaniel's theology) or someone who is part of the Pilgrim Alliance, a militant state that developed from McDaniel's religion (which I suppose can be further divided into people who serve the Alliance government and those who happen to live on their planets). Individual "Pilgrims" might be one or more of these things. For instance, Blair is a Pilgrim because he has the genetic ability but he doesn't follow the McDanielite religion and he isn't a citizen of the Alliance.
Now the history.
Between today and the end of the 23rd century, humanity reaches out and colonizes our own solar system. We build massive ring-shaped space stations and then outposts and colonies. The first terraforming begins in 2079 and the first completely self-sufficient colony, Olympia Station, is founded in 2161.
Several things in this time give rise to the Pilgrims.
The first is the political situation. Earth becomes increasingly isolated--the Outer Planets become a stronger unified body and they begin to resent the fact that they are responsible for providing resources, manufacturing, etc. for the home world. Then in 2219 the First Great Pandemic hits. Earth and the moon are ravaged by a new disease and the Outer Planets Policy Council decides to quarantine Earth--no one can visit or leave the planet. This limits spread of the disease but further cuts ties between space-born humans and those on Earth. It also means that further colonization is being done by the populations already in space and not those on Earth. That's where the second important factor comes into play.
Throughout these three centuries of colonization humans have found that succesful pregnancies on space stations are much less common than on Earth--stillbirths are much more common and conception is harder in the first place. What's happening is that space is selecting for Pilgrim's innate ability to measure graviton fields. The same thing that allows offspring to survive low-gravity pregnancies will later give their descendants the ability to measure jump lines. This isn't fully understood for several generations (since, after all, there are no jump points yet) but it makes the particular gene increasingly common in space... and that's further aided by fact that an influx of genes from Earth slows down and then stops entirely due to the quarantine.
Then, around the turn of the 24th century, a scientist-philosopher named Ivar Chu McDaniel gives this all a religious overtone. In his writings he claims that the now-identifiable unique abilities of those born in space combined with the terrible plagues on Earth are proof that those living in the outer colonies have been elected by God. McDanielites are, he says, destined to leave the solar system and anyone remaining is damned.
His views come at a unique time which allows them to gain traction quickly--the outer planets have supported Earth with food and resources since the Pandemic for little recompense... and in 2304 their scientists make an amazing discovery: the first FTL drive. It's called the Morvan or "Hopper" drive, and it's the first step that will eventually lead to the modern Akwende Drive. Hopper drives are comparatively dangerous and notably slower than jump drives, but they allow mankind to reach the stars in months or years rather than lifetimes (slower-than-light colony ships with fusion drives had been dispatched previously on occasion, but they would take generations to arrive anywhere). McDanielites begin leaving the solar system in droves for twelve star systems in the Sol and Vega Sectors. They're the first major colonies established and so they give birth to a powerful star nation--the Pilgrim Alliance.
The concentration of Savant abilities, outer planets resources, a general advantage in terms of scientific standing and a religious furor gives the Pilgrim Alliance an enormous advantage. Other humans begin colonizing the galaxy, but it is a much more slipshod thing--hopper drives have a high casualty rate when not operated by Pilgrim navigators and Savants not aligned with McDaniel's church are few and far between. Still, the sheer number of lesser colonies established in this manner worries the Alliance.
So in 2462 a heavily armed Pilgrim Alliance warship arrives at Earth with an ultimatum for the Terran Confederation--agree to a treaty that effectively prevents further colonization or face war with the vastly superior Alliance. The "Treaty of Luna" officially bars Terran Confederation colonies from being established within 300ly of Earth... beyond the practical range of the hopper drive.
... but not the jump drive! With a higher population spread over more planets the Confederation catches up with the Alliance in terms of military power and organization within the next century. Then, in 2588, they turn the corner--the invention of the Akwende Drive allows relatively safe space jumps across great distances. A century of building a resource base, unified government and advanced technologies means that hundreds of colonies are now established in a matter of decades-- all outside the 300ly barrier created by the treaty.
The Alliance is outraged--and they still believe themselves the military (and moral) superior of the Confederation... the stage is set for war.