
What I imagine is: The Player HQ has another office, where every race has a "Black Market Dealer" of Blueprints. Basically a faction representative without the rep stuff.
He will sell you all blueprints, always - but for a cost. Blueprints there are double as expensive.
That should be a relativly easy (and game-safe) way to allow you to do a "Split kills all" game or one where you role play your own faction without missing the important stuff.