What's the difference between a country and a military organization? Military leaders can be replaced a lot easier.
There are plenty of people who believe that a country
is a military organization: that's how it started (put, crudely, by ancap "philosophers" as a protection racket writ large) and that's basically all it was up to the nineteenth century in most of the world.
And there are plenty of examples of military commanders with...mediocre reputations (deserved or undeserved) who have gone down in history as having relied on more able subordinates. The classic example is Paul von Hindenburg and Erich Ludendorff; my personal favorite is the Athenian duo of Alkibiades and Thrasyboulos.
In many of these cases, the higher commander was not merely a military technician, to be replaced by a better technician if available, but was a symbol to his men and even a political touchstone. Historians still debate Hindenburg's actual role in the partnership he had with Ludendorff, but no one disputes his
importance: the man was a cultural icon even while he was still in the army, due to the victory of Tannenberg, and remained one of the most beloved people in German political life for decades. He rode his reputation into the chancellorship under the republic, after all. And few historians would dispute that Ludendorff, although a gifted staff officer, was awful at interpersonal relationships and far too high-strung to even stick with his own plans once implemented; he needed Hindenburg, at the very least, to convey calm and imperturbability, to keep him anchored in reality, and to make him more palatable to the rest of the staff. Those are functions most often associated with a "figurehead", yes? But they made the partnership work, and it's one of the most well-known and successful of its type in all of military history.
But let that go. Talking about generalized nonsense gets us nowhere: the specific example of the Inquisition is what matters, and I, for one, am not sure that the Inquisition's leader
can be replaced so easily. Cassandra certainly seems to be using him/her reluctantly; if she could get away with running the show herself without an Inquisitor, I think that she might have tried. But the Inquisitor survived the Breach's opening, limited the damage, came away with a unique power without which there is little to no chance of closing the Breach, and has already become known as a symbol of hope throughout southern Thedas around which loyal forces can rally.
I mean, I'm not suggesting that the Inquisitor
should be some simpering, tied-up sub for Cassandra, or that that would be plausible - #notmyfetish, among other things, but yes, I know that "simpering" and "sub" and bondage do not always go together - but "figurehead" is actually quite close to what I think the Inquisitor might very well be
anyway, at least in the early going, and I think it's precisely that figurehead status that makes him/her
irreplaceable.