Truly the evidence of the OP's claim is overwhelming.
Wait, what?

Not that I don't agree, but surely some evidence is required to make such a claim.
Personally, I like the chantry as a fictional construct. It's a very well designed religion, and I love the idea of the Chant of Light and the passages we've had the opportunity to read so far (and the Chanters, no vows of silence for them! *grin*). I also think it makes sense that something like the Chantry exists, and find it logical that most people believe in such, simply because the supernatural DOES exist in Thedas.
In short, people turn to the Chant not only to explain Bad Weather and disease and Bad People, but also actual tangible demons and magic. It becomes rather difficult to maintain a natural materialistic outlook in such an environment.
Of course, the truth is that all those things CAN be somewhat explained rationally without relying on a baseless religion (the fade and attendant phenomenon are part of nature after all)... but it would take a far greater effort to maintain an atheistic outlook. Hence why my characters tend to be religious (except perhaps some mages, who have a deeper understanding of the fade and such).
But anyway, I digress. In what way is the Chantry doing more harm than good?
It might be misleading people, certainly, though I think the nature of the fade to manifest things in accordance to people's belief probably means that Chantry leadership is not simply making things up. They probably truly believe what they preach, and see the Chantry as more than a means for controlling the population.
On the other hand, they do provide a tangible benefit through their militant arm: they safeguard society from mages. Of course, they do that by oppressing mages, but there's no denying that it does succeed rather well at this (despite sporadic outbreaks, mages are kept segregated and the general population is kept safe by the Chantry and its Templars).
So on that last count, would the general populace view the Chantry as doing more harm than good? Certainly not. So why would it be "thrown out" of Kirkwall?
Itkovian