I had a similar problem. I created a simple system of spending allow Player Characters to spend 1 Fate Point (once ever, for now , for either 2 basic NPC cohorts (meaning, a Novic Navigator, Novic Tech Priest, Hired Gun, Spy, Adept, etc.) or 1 Fate point for one advanced NPC (like an Orc, Ogryn, Eldar, Kroot, Oathsworn Bodyguard, Pirate Captain, Astropath, etc.) . XP/Skill/Talent awards would be based on what actions that NPC did. Meaning, if the characters and the NPC were conducting allot of boarding actions and succeeding, the NPC would probably get a permanent +5 to BS, or +1 Wounds. These NPC's would also have 1 Touched by the Fate point to represent how important, yet minor, they are to the story line.
Of course, you can always allow players to roll up NPC's using either Dark Heresy rules or Rogue Trader (but remember Rogue Trader char's are considered 5,000 xp DH char's) for the cost of 1 Fate Point. These are options, but all in all, it's about having fun. So the choice is up to the players and the GM to agree and decide upon.