I agree with you. There is a distinct possibility that a Knight-Commander, instead of submitting to the Cahntry's will, will decide by himself or herself that the Grand Cleric or the Divine isn't fit to give them orders, an obstacle to their duty and thus it's morally right to oppose their orders and do "what must be done". Even if their original duty came from the Chantry itself.
You know, scrap the "distinct possibility" part, since it has already happened: Lord Seeker Lambert, without any need for a red-lyrium-induced madness, did exactly that. Since I believe Lambert was honest in his actions, I think it's a clear sign that the system is broken.
Well, the Grey Wardens are also an organized international system, and that's why I'm a supporter of the Inquisition becoming the new managers for the Circle system, or whatever they choose to call it in the future.
It's not a matter of good intentions and progressive ambitions. It's that by the time DA:I ends, the Inquisition could be an international force, with armies, fortresses and public legitimacy after solving the Veil Tear crysis, not unlike the Grey Wardens after the end of the First Blight. Support from pre-existing actors only matters if they have enough power to oppose you. With the Inquisition having the actual monopoly on violence in several key places, the Chantry without its teeth and their most adherent supporters weak after a civil war (with the distinct possibility of the victor being indebted to the Inquisitor), their room for negotiation might improve a lot.
But as I usually say, it's just an idea.
The problem with the Grey Warden comparison is that while the Grey Wardens are an international organization, they are not an international system. At the end of the day, they are too small, marginal and marginal to serve as a model.
In the first point, the Wardens aren't a major military force in most places. Unlike the Templars, which effectively are an international army with multiple military bases and troop movements, a force of national concern if they wished to be, the Wardens... well, aren't. The Wardens are a elite force, but a small one, and little suggests they could crush nations if they wanted to. Even their right of conscription is, as a matter of political practicality, used sparingly- and, of course, heeded only in so much as the nations respect it in a case of 'we will give you whoever you ask for as long as you don't ask for anyone we won't give up.' The Warden presence is small and limited: by comparison, the Templars are magnitudes larger in scope and scale.
In the second, the Wardens are a marginal force. They are insular as an organization, stick to the margins of civilized areas and are rarely seen by most, and frequently go to places like the Deep Roads where no one else has an interest. On top of that, they have relatively little political might- the Anderfels are the big exception, obviously, but until Amaranthine the Wardens have never had a role in the political establishments. Templars, by contrast, are much more heavily involved in the day-to-day workings of society: they are far from politically marginalized through their partnership with the Chantry, serve and recruit publicly with many ties with the masses, and the jobs by necessity bring them to interact with masses, from Chantry guards to mage-related concerns in cities. Wardens, secretive as they are, are rarely seen or involved: Templars are far more present.
The point of this contrast isn't simply to emphasize the difference of scale: it's to highlight the difference in an organization and a system. Both groups are largely apolitical, purpose-focused, and have some secretive traits about them, but there's a key difference between them. The Wardens are not viewed as particularly threatening or worrying to the nations of Thedas because they aren't that much of a threat- even if they did get involved, their actual power would be limited. The Templars are not viewed as particularly threatening or worrying ot the nations of Thedas despite the threat they can pose: the Templars have had a much greater position to be much more interventionist and and active than they have been, but this does not dominate their reputation despite their already considerable involvement with society.
The important factor here is credibility and legitimacy. The Templars have become a part of the international system because of a millennium of collective involvement. That's not something that can be built in a year: international organizations can't just be expanded with new duties to replace a system. The institutional know-how, the popular legitimacy, the simple experience and acceptance doesn't come that easily.
It's easy to say you'll replace the Templars with a new group of Templars with a different name. It's much harder to actually do it off of any group in Thedas.
We shall, of course, see about the Inquisition. I doubt the Inquisition will ever gain a monopoly on violence, and suspect we'll be finangled into alliances whether we would like them or not. But the terrain limitations of the game alone work against setting up a new international system in and of itself: too many places far out of reach to affect.