Oh, you mean a Commissar? Well... the Imperium has something vaguely similar to that. >.>
Commissar - Lexicanum
That said, the Imperium's Commissariat has jurisdiction over all military branches, with the exception of the Adeptus Astartes (space marines), Adepta Sororitas (Sisters of Battle) and the Skitarii(soldiers of the Tech Priests of Mars). Rogue Traders, however, are not part of the Imperial military. They're explorers and advancers of Imperial influence through trade and encounters with the alien and the unknown, and often times above the law. A commissar would have no power over a Rogue Trader, but that isn't the only place a staunch Imperial could fill on a vessel.
You also have the missionaries of the Ecclesiarchy. They are full priests, but have no jurisdiction over the Rogue Traders, but they are often given a place as a crewmember aboard their vessels, with a twofold purpose: one, to spread the word of the Emperor to lost populations of humans they discover, and two, to serve as religious ministers to the crew itself. They have no power over their captains, but they still serve as a voice in favor of Imperial doctrine.
Wayward members of the military who have become lost and separated from their unit or vessel, or perhaps are one of the lone survivors of a disastrous defeat, could be recruited to serve in the crew, at least until they're returned to Imperial space to muster back into service.
Planetary nobility, while not given the same privileges as a Rogue Trader, could theoretically have the funding (and freedom, should they be a younger child not in line to inherit a governing position) to go off adventuring in the far reaches, and find themselves needing to side with the Arrow of Artemis and her captain in an hour of need. Their devotion to the Imperial way of life varies, of course, and they hold little power outside of their world aside from the power of the almighty dollar-- or throne gelt, or "throne" as they're called in the Imperium.
Just a few options available. You COULD still play a commissar, but know that whatever you decide on, they're not gonna have any power over a Rogue Trader like Glory.
I don't think Book is comparable to a thorn-in-side adversary, though. I think the idea has merit, but let's talk over exactly what you want, and what can be done.
