For the first few games, I'd probably NPC the RT like most others have said, but lead the game in a direction where something happens to the RT and the players have to decide who's boss (even if it's all of them).
In future games though, I'd leave it up to the players to come up with something ahead of time, or if no decision can be made fairly by them, base it off their character. I'm thinking characters with the highest Fellowship, and/or really good Charm or the Leadership Special Ability that the Forsaken Bounty Rogue Trader had.
Of course, exceptions would be made for truly skilled players, or if the highest Fellowship/Charm/Leadership character was a noob to the game/roleplaying.