General User wrote...
Since I'm not familiar with the City Elf Origin I can't really comment on it. I will say though that I wouldn't get too caught up with the elves. It's hard to help people who don't want to be helped no matter how much one might try. Think instead of Brother Burkel, the Chantry missionary to Orzammar.
The thing about Kirkwall is that Hawke doesn't really interact with the Chantry outside of high politics (and politics dirties everything it touches). We don't get to see the Chanters collecting alms, or the missionaries tending to the forgotten like we do in Origins. Does that mean such things are not taking place in Kirwall? I highly doubt it.
I'm not saying that the Chantry is perfect (it is run by mere mortals after all), and there surely are things they could be doing better. But whatever failings it may or may not have, the Chantry is undoubtedly one of the primary and most powerful forces for good in Thedas.
The problem is that like any group of humans, although you're going to have some who are honestly just trying to help, there will be others such as Petrice who take their faith to be more than just faith, and cannot stand the idea that faith and belief vary from person to person. The Qun is highly successful in conversion, so she views the Qunari as a threat. Unlike Elthina, who despite the rest of her shortcomings at least understood the need for tolerance.
That said, the same thing I say about mages applies here; it is a simple fact of human nature that there are more people trying to good than trying to do evil, so in the end there will be more DAO sisters than Petrices, and at the level of sisters and mothers the chantry is a net positive force in Thedas.
The issues come in when you consider that in some nations the Chantry is actually involved in governing the country. Ferelden keeps faith and politics separate, with the result that there are no serious problems caused by Andrastian religion. However in Orlais, the Chantry has influence over politics too. This lead to the war against the original Dalish, as the Chantry couldn't stand the fact that the elves worshipped different gods, and wouldn't allow their military arm - the Templars - on their land.
The Templars themselves are the single biggest problem with the Chantry. By maintaining a standing army, the Chantry ensures its rules are enforced. Ignoring what they do to mages, it is simply a bad idea for an organization based on faith to have a military component. Humans are inevitably wrong about pretty much everything regarding the divine, as they are only mortal and simply cannot comprehend it. As such, everyone who has faith has different ideas, whether they worship an entirely different pantheon such as the elves, don't believe in any higher power such as the Dwarves, or just slight variations amongst those of the same religion.
Now if these people disagree over something relating to their faith, normally nothing would come of it. (And since there are as many variations of faith as there are people, there are going to be disagreements.) However, when one organization has an army, a simple disagreement can turn into a terrible tragedy, such as what happened with the Dalish. Not to mention what happens if you allow Burkel to create a chantry in Orzammar. If the Templars didn't exist, and if the chantry was not involved in Orlesian politics, the elves could still be living quite happily in the Dales.
Now that the Templars have dissociated themselves from the Chantry post DA2 and Asunder, all that is left to do in DA3 is remove any political influence the Chantry still has left, and it can become that force for good you describe.