That's an double standard. The Chantry did the same things that you are accusing people of trying to do here. Bottom line is, victory is written by the victors. The Chantry won their wars before and their word became law. The same will happen if the Inquisition succeeds in destroying the Chantry (if we are truly given that option that is).
....Why would I use the same tactics of an organization whoses methods I disagree with? It's called learning from your history. Watching the Chantry and other groups impose their will on people without the consent of the governed has shown me how problamatic that is in the long run. Now, you are insisting the Inquisitor do the exact same thing 'For their own good'?
Yeah that'll end well.
Because it would be rebuilt at a smaller scale (in villages) with slight variations (different opinions) which would make it harder to gain political power as a single entity. And it would be closer to the believers, better fulfilling its role. No need for an extra-big organization...
It might start off small, but how long would that last? Are you going to put the previous Chantry leaders too death? I mean if you let them live how long before the ralley the various smaller churches into one larger organization? If you do put them to death you likely make them martyrs, and new people will rise to take their place, possible in secret, out of your sight, until the new Chantry has the same type of power and influence as the old.