The inquisition technically holds no sway over a RT, period. The Imperium is a feudal system, and they are of equal rank. To legally take action against the other, they have to go to someone of HIGHER rank, which in both parties cases is only the High Lords of Terra.
In addition, Rogue Traders are EXPECTED (and all but required to to their job, really) to be heretical to some degree. Especially in any dealings with Xenos. As the books state, many in the inquisition would love to declare most RTs heretics, but they simply aren't allowed to.
The inquisitor(s) in question are at a further disadvantage due to the very nature of the Inq not being anything resembling a unified body. Unless he's gone completely off the rails and their is DAMNING evidence to this fact (major traffiiking of halo devices and the like to parties other than the mechanicus), the RT isn't up against "The Inquisition", they are up against one inquisitor or a small cadre thereof, whose influence may quickly go to crap if they move against a RT that other inquisitors feel is legit. Hell, its entirely possible the RT might never even learn of the inquisitors ire, or have to get involved beyond a quiet word; RTs being what they are and going where they do they might well have friends in the Inquisition....
Whereas the RT has (unless the warrant is newly minted) an entire dynasty to back him, likely including what would amount to a warfleet and certainly including vast economic influence and alliances.
And if the RT is doing what he is supposed to and operating primarily on the outside of the imperium and the fringes thereof, if the Inq goes after the RT and catches up to him out there, where the RT "speaks with the voice of the emperor", the RT actually outranks the inquisitor and can, technically, deal with the inquisitor as he sees fit.
Short of the aforementioned damning evidence, an inquisitor's only real recourse is to...
1. Use assasination and well-concealed catspaws to try and take the RT down.
2. Find another RT willing to take them on (with the knowledge that if it isn't a clean job or they fail, it could lead to a war between the dynasties as damaging as an Inquisition War.
3. Gather whatever allies they can bring to bear and try to take out the RT as quietly as they can themselves, with the knowledge that, from a legal standpoint, they are technically in the wrong and there will be few if any repercussions for the RT killing them in self-defense, whereas if they succeed and word gets out, the Dynasty might seek revenge.