I don't mind them having a firmer voice what i do take issue with is granting ultimate authority of the Templars and Seekers to the Divine; If anything the current Crisis proves that changes in leadership can cause issues with existing policies and stances. Ultimate Templar Authority should rest with the Seekers and while the Chantry should have a voice in the matter, it shouldn't be primary for their faction. In fact i'd argue that Keeping the Circle out of Chantry control is one of the few measures i'd agree with most pro mages with. Justina proved why its ultimately a bad idea; She crossed a line, Lambert disolved the accord and the mages under a short sided grand enchater marched to war.
The entire crisis can rightly be pointed at the Divine.
Moving along though; You propose weakening the measures that have kept magic contained, while as i said prior have issue with them maintaining a stronger position within the circle; The Mages should have no power beyond the circle. No titles, No Lands, No business, No stake in politics, Economy or Religion.
Furthermore there is nothing to suggest the Inquistion is anything more then a temporary measure to combat the current crisis; it likely will not be around to involve it self overly in the mage issue and it shouldn't, Its ultimately a responsibility that falls to the Templars.
I would agree that the current Divine has done a crap job. She's too complacent.
However I am willing to believe that a primary reason of the Circle's fall is due to bad leadership which is another issue within Thedas in where people of power simply are not held accountable for their decisions.
You mentioned Justinia's action and that further points out the flaw of the old system in where the Divine and the Seekers of Truth simply have no power in checking the power of the Templars hence the back-handed channeling with the Divine's use of her agents.
I believe the Divine can play a role as her voice commands respect from the populace. This is needed. She has no actual power to speak of but her influence is undeniable. So lets use her to promote a more sympathetic view of mages as a whole rather than one of fear. Lets use her influence and her agents to hold the Templars in check while dissuading extremism. Combine this with the martial arm of the Inquisition and it should help keep the peace.
That said, I agree the Chantry should back off of the Circle. As I said, let them control themselves while being held back by the Templar, the Seekers, and the Inquisition.
I agree that mages should not interfere in the country itself. They keep in their own circles and if they dabble in politics, it will be their own.
As for the Inquisition. I daresay that organization is here to stay. I doubt it will simply fade when the dusts settled.