The Imperium is far more likely to pull out entirely - possibly firebombing the place from orbit if they don't think they can counterattack quickly - than work out any sort of deal where an alien empire even
seems to be governing one of their worlds. That's a pretty big no-no, even for those members of the Ordo Xenos with a more Radical bent.
Having said that, there's a lot to be said for 'retreat and live to fight another day', so long as there isn't a Commissar watching. Why would the Tau agree to continue letting the planet supply and serve the Imperium, so long as they got to run day-to-day operations and operate freely? What's their game here? In the past, the Tau empire has been more than happy to to outright conquer planets...so why not this time? Clearly, the acolytes are on the verge of uncovering some sort of sinister xenos plot, and escaping to inform their master of the situation and gather additional forces is far more important than making a suicidal last stand. They're in the Inquisition, after all. That's their job. Let the Guard and Navy do whatever they want, so long as the information returns to someone who can do something with it. Traitors will be dealt with accordingly upon the Imperium's return.
At least, that's how
I'd spin it to the hardliner elements of the party, if I was playing.