Yeah, like Stabby said, as long as they operate outside the imperium even the Inquisition really can't gainsay a RT. That stated, there isn't much point to playing a steriotypical Sister on a RT ship, unless the goal is to foster bickering and eventually be fired out an airlock. A more open minded sister though, sure, why not?
I've always taken issue with that idea. The Imperium of Mankind does not exist inside the Koronus Expanse, but the Rogue Trader himself is still an Imperial citizen. The Inquisition is free to say that your actions have damned your soul, and label you a heretic and execute you. The law is handled by the Adeptus Arbites, who indeed do not have jurisdiction to pursue you outside of the Imperium. The Inquisition is concerned with the moral integrity of the Imperium as a whole, and as long as you are an Imperial citizen, they should be able to judge, condemn and execute you if they see fit.
It's more the "out there, there's not much they can do" mentality. The Inquisition doesn't keep a bunch of its own ships, they wouldn't have Arbites assistance out there, and that just leaves them, if they feel like going out, and their Acolytes, if they aren't busy rooting out trouble in the Imperium's space. If an Inquisitor can pull together his stuff, and get to the Rogue Trader, he can certainly pull a plasma pistol on him, and gun him down, but he might have to fight the RT's crew, and not have all of the resources he's used to lugging around. In IS, he can turn a battlefleet on your ship, or throw an IG regiment at you, ban any Imperial facility from allowing you to dock for resupply and repairs, but out beyond IS, he's only got what he can bring with him. It's not "can he judge?" as much as "can he deliver judgment?" At least, that's how I've always seen it.
Being the douchebag I sometimes am, I've already planned that, if a group playing under me goes completely off the rails, and starts doing stuff that truly endangers the Imperium, or a sector of it, they'll get a warning, or two, and then I'll sit back. If they keep going, sometime, when the RT is alone in their quarters, talking to their second, I'm going to ask for the second's sheet, and then reveal that this individual is actually a Callidus Assassin (the unknowing second's player's surprise will help sell the scene), who will then proceed to try and kill the RT. I don't expect him or her to be able to best a full Callidus, and I can see an Inquisitor doing this. You stopped at a port, picked up new ratings and supplies, and someone snuck in. How long has this Assassin been playing as your second? Who knows? Do they just run off of the ship, fake you into grace, or die while blowing the whole vessel apart? I would put it off till they were irredeemably tainted, of course, and give warnings, but the Inquisition's reach is long, even beyond the Imperium's edge.
Where exactly does it say that trading with Xenos is heresy when the Emperor himself specifically gave rogue traders the right to do so? If that is indeed the will of the Emperor, Why would a sister have a problem with it? Particularly if she was told about this fact before she ever boarded! My basic thought was that the sister would of course need to modify some her more puritanical teachings. This might be possible if she could be shown that this particular individual has a remit from the lords of Terra (Which would include her beloved Ecclesiarchy) to do so! Certain other activities might stretch her tolerance but not those specifically permitted by the Warrant. Now Piracy or dealing with ACTUAL heretics, (Like say, the denizens of Iniquity) might push her over the edge. But then again, It should push ANY reasonably faithful Missionary over the edge as well! Remember that a Missionary has the same Driving faith ("Pure faith" if you prefer) that a Sister does. Properly played, NONE of them would stand by while their RT drifted into heresy!
The Emperor was also a psyker, and the Ecclesiarchy hates them. Actually I would imagine that they don't like Rogue Traders much in principle since they are by definition violating the whole "ignorance is bliss" thing..
Sisters are puritanical by nature, the hardest version of the "kill the witch, kill the alien" ideology.
I said the Faith Powers from Blood of Martyrs, which are quite a bit beyond what Missionaries get and a lot more "space cleric magic" than the RT ones, which can mostly be interpreted as products of fanaticism..
Anyway, that's what I would do if I were the GM.
Warning, don't mention the Emperor's obvious psykerdom. I say that because I brought it up on the OW forum, and was reminded that most people in the Imperium don't know that; he had holy powers, not warp-fueled possibly sorcery. Personally, I sometimes forget what most in-fluff people know, compared to what I, the reader know.
As an aside, depending on how you view the Emperor, again this isn't D&D; He's not an active God, in some ways, so your powers might not fade. Also, many practices of His faith, starting with the faith, are the opposite of how He felt, so either way, He might not take any powers He is granting you away, even if they should seem to go, as you seem to break faith with the Ecclesiarchy, which is NOT Him.