I like the "Inquisition-as-reinforcements" idea.
And, if you want, after the battle's done, the Inquisitors can call for the PCs surrender, to stand for inquisition into this whole sordid affair.
(But given D&D magic, it ought to be a pretty simple explanation -- find cleric of 7th+ level that the Inquisitors trust, surrender all items [to make sure nobody's wearing a doodad of nondetection or the like], have cleric cast discern lies on PC, PC purposefully fails save, and answers questions. End of misunderstanding.)
(Assuming the Inquisitors are trustworthy & the PCs innocent of wrongdoing, of course!)