Anyway the whole time the Inquisitor has already lost control of the Inquisition.
You disband , or you give your power to Orlais/the Chantry.
Nothing else was on the table.
Except that you aren't giving over your power to Orlais, their government has absolutely no role or control in future Inquisition affairs.
Neither are you really giving power over to the Chantry. The Inquisitor makes it very clear that from this point on the Inquisition will operate as Divine Victoria's personal honour guard and answer directly to her.
In other words, the Inquisition does not answer to anyone in the Chantry but Divine Victoria herself. This is no different from what the original Inquisition did when they reformatted themselves into the Seekers of Truth.
Actually, I suspect that the wording itself might have been phrased that way deliberately, that we swore to serve Divine Victoria... meaning that the Chantry and any future Divine should not expect the same automatic loyalty from them. If you pick the rather more aggressive option, the Inquisitor makes it very clear that for now, their playing nice is merely a temporary arrangement to placate them.
(Sure, this leaves it open that in time, the Inquisition might eventually go rogue much like the Seekers, but shame on that Inquisitor, not us).
If the Inquisition continues, I suspect that they are taking the Warden/Seeker approach, chosing to operate from the shadows to better prepare for future crises that demand a non-government organisation to step in and act, allowing them to avoid any red-tape.