At the OP's question-
I think the Chantry gets a surprisingly generous take from the Devs- certainly much, much kinder than what it easily could have been.
While it's clear that the Devs have never intended the Chantry to be flawless or universally beloved, they deliberately and greatly avoided a common trope of 'the church of evil,' in which the organized religion of X controls people by superstition to the public detriment and the church's own interest. Quite often organized religions are neutral at best, malevolent at worst, and almost unfailingly opposed to rationalism in favor of superstitious (and ultiamtely baseless) fears.
While myth and superstition do factor into the Chantry, instead of baseless fears and stigmas the Devs gave the Chantry real and credible fears, with real and rational basis for their actions. The Chantry is in many respects the primary international security establishment for Thedas, a sort of more-capable UN which organizes collective efforts, collective defense, and mediation efforts across most of Thedas. It manages real security and safety concerns in the form of the Circles (even if it comes down more on the side of a security state than maximizing human freedom regardless of cost), it organizes international coalitions against real military threats to common security and freedom, and it's a key legitimate actor and moral authority whose presence and words are shown to temper many actors.
As far as the religious behavior and doctrine go, the Chantry is about as kind and gentle as any major religion ever gets. Conversion is voluntary, with most negative pressures being from the lower level rather than condoned by the clergy, heretics and dissent are allowed (if not enabled), the only two known cases of religious purging/cultural genocide were in direct response to major wars seen as unilaterally started by the other religion (and even then heathens were given the choice to recant their professed beliefs and keep their heads low and on their shoulders), and there's no meaningful history of the Chantry itself spreading the Chant by the sword. (The Orlais Empire under Drakon One is a related, but ultimately separate, entity.) Radical clergy are broadly kept in hand, the leadership maintains a healthy cadre of idealist individuals in senior leadership positions to balance the pragmatic security concerns, and the Chantry's military arm has an exceptionally notable public reputations thanks to providing public security services aside their own task-specific duties.
There's plenty within all that to take issue with, to be sure, but the Chantry is about as beneficial as any organized religion or ideology can be. It can honestly be described as well-intentioned and providing real benefits for most of the populace under its influence- despite being in a crapsack world and facing many real and exceptional dangers that could easily justify a much, much darker and cynical take. It's also helpful that most of the Chantry's worst actions, complicit or otherwise- historic issues such as the fall of the Dales or the Qunari invasions are not even in living memory, let alone the current context of the institution.
The Chantry has a better historical rap sheet than most real world institutions, including most western governments, while its current iteration is close to ideals of enlightened self-interest: it's interests are closely aligned with peace, stability, and even being open to reform.
That's a very generous depiction, and not one the writers had to offer it at all.
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