The Chantry is in sufficient disarray that Cassandra decides that the Inquisiton should be neutral, and the Inquisitor will cement bases of power throughout the regions with soldiers and political ties. All this considered, I'm not certain that the Chantry will ever wield the same level of power that the Inquisition can potentially acquire, especially once their former militant arm or their Circles of Magi become part of the Inquisitor's organization.
Queen Anora's initial attempts failed, as I pointed out, but she did make the attempt in the first place; King Alistair succeeded because he took further steps by giving the elves a voice at the royal council, despite the controversy that ensued among the humans.
So you're suggesting that the Inquisitor should take further action to nullify the threat posed by Orlais? I don't disagree that this might be required to guarantee the sovereignty of Ferelden and an independent Dales.
Unless you've got developer quotes that support your assertions about the Inquisition breaking free of the Chantry due to the Chantry being in disarray, you aren't being very convincing. I would agree that Cassandra is following Justinia's wish in creating the Inquisition, and that she takes the Inquisition off the ranch to prevent the disarray in the Chantry Leadership from focusing the Inquisition on the wrong goals, but none of that even remotely suggests that the Chantry itself is in any danger of losing their place in Thedas.
Anora made an attempt that was convenient, and abandoned it when it stopped being so. That's not a quality you want to look for in an ally. And Alistair, regardless of what he thought he was doing, still failed. The Hinterlands are Redcliffe territory now, and "Arl Teagan" doesn't sound like a Dalish name to me. Even with the theoretical elven advisor, Alistair was powerless to circumvent the will of his people. Good intentions and a cup of coffee are worth exactly a cup of coffee when you don't follow through.
What, exactly, makes you believe that things would go any differently in elf/human relations if those 'knife-ears tried rising above their station' right there on the other side of the border? What makes you think the people of Ferelden would tolerate that any more than they did the elves setting up shop in Blightlands? Blightlands. The humans of Ferelden hate elves so much that even letting them settle on poisoned ground was unacceptable. And if the people of Ferelden did take issue with it, what is the monarchy going to do? Send the army after their own people on behalf of some 'knife ears'? Yeah, no.
An independent dales would be a rash on the Northern Ferelden border, and eventually it would get scratched. Probably with the help of the other human nation in the area, because when it comes to elves, humans are pretty much united on the proper course of action.
All I'm suggesting is that if you think Ferelden is going to protect a nation of elves from Orlais, you are gravely mistaken.