It seems unlikely that the crew is entirely Project personnel. A few points:
- The Vesuvii aren't secret assignments; they're /the/ major symbol of the Confederation's post-war rebuilding effort, debated in the Senate... and being built at L5, for Gods sakes. You could likely spot the construction with the naked eye on Earth. The Confederation is an open Democracy with plenty of civil oversight; if the fleet's massive new flagship were apparently being crewed by *no one*, it would come out.
- There aren't 7,800 'GE' people to begin with. The 'first generation' is four fighter wings worth of pilots (~400 people). The 'second generation' (ground crews and a battalion of soldiers) were their offsprings. These people would have had to be born in a very narrow window, between 2653 and 2657, in order to be adults during Wing Commander IV. Even if there are 200 couples producing a new child every nine months in that period you end up with barely over one thousand -- which would just cover the ground troops.
- Following on the above, the Project didn't even crew *Axius* with exclusively 'Black Lance' personnel. Blair is recognized by a security guard who had known him on the Concordia -- even that most secret of bases was an ordinary duty station. To everyone involved, save the leadership, they are part of a legitimate Confederation military operation.
- Similarly, a ship doesn't simply require 7,800 warm bodies... it requires 7,800 different types of particular expertise. The necessary expertise comes from a vast interconnected system of Naval training and practice. Tolwyn's tiny secret organization couldn't possibly produce the sheer diversity of training that thousands of Navy postings, service academies, technical schools, development programs, etc. do. He's training pilots, infantry men and fighter ground crews -- not radar officers, riggers, weapons loaders, mechanics, reactor crews and so on and so forth.
- Remember the Lexington and the Princeton - two much less prestigious postings co-opted by The Project for launching Gen-Select strikes... neither of which were Project-crewed. Tolwyn's forces provided their specialties in both cases: ground support crews and pilots, nothing more (not even a captain!).
- There's nothing necessarily subhuman about the GE crews to begin with. Tolwyn didn't put out a sign-up sheet for cold-hearted murders with no sense of decency; it's a pre-existing project developed for fighting the Kilrathi that he co-opted... and the majority of the crews were born into the thing in the first place. We know from Tolwyn's speech that there was internal protest over using the bioweapon... we see Colonel Roberts speaking against the Project at Tolwyn's trial... it's not some universally damnable group of people.
More to the point, though: if *you* don't know who's crewing the Vesuvius then *Blair* certainly doesn't when he's making the decision to destroy it.
Remember: Blair isn't perfect... and a pig is usually a pig: when we see Confederation-uniformed crews on a Confederation ship, it's likely the intent was to show that they were Confederation crewmen and not /secret/ Black Lance members.