The complete lack of 'freedom of thought' is an exaggerated point, as Iron Bull explains. The goal is that everyone works for the betterment of society as a whole; people disagree with what that means and it's the duty of the priesthood to interpret and decide.
The fact that there is internal disagreement and interpretation says to me that there is room for change, and perhaps, co-existence.
Now, in character, my inquisitor would oppose a qunari invasion when and if that happened, but he would first and for most try to avoid it's to begin with, and secondly, would work to end it under peaceful terms once it got started. There's more to be gained through cooperation with the qun, if such a thing is possible, than there is in a war that may or may not be winnable.
Taking one person's word on an entire culture is never a good idea, and when the culture breeds its followers to think the same thoughts, it's even worse. I heard what Bull said. I've heard what every Qunari has said in all three games. It doesn't change the fact that, when it really comes down to it, you are either with the Qun or you are forced to be with the Qun. I understand what the Qun is - trust me, I really do. And there's always room for change in any culture, because that's what makes people people. Only the most rudimentary logic-based system has no room for internal growth. The issue here isn't that the Qunari may or may not be able to coexist with the other species of Thedas - that's already been shown to be possible, since it happens everywhere they go. What they can't - at least right now - do is coexist with the separate ideologies of Thedas. There is only room for the Qun in the Qun. I really thought that had been made obvious. Even Iron Bull said that the party members who would do well under the Qun, if they didn't die fighting, are Cullen and Cassandra because they love following orders. So while the "freedom of thought" argument is exaggerated, it really isn't that exaggerated.
Edit: On another note, I do agree with your more recent post about the loss of the Qunari being a tragedy. I certainly don't dislike them. I just don't see peaceful coexistence being an option with the Chantry, Tevinter, or the more free of the Free Marches. And when it comes down to it, while I don't hate the Qunari, I don't like them as much as I like the other guys.