Too often the quote "Magic should serve man, never rule over him" is used to focus on the "never rule over him" part and forgets the first part which is a call for mages to go out and do the makers work. The chantry for too long has allowed a stigma to be attach to mages, they are too dangerous. As if mages were some type of curse from the maker. That type of dogmatic discrimination has been hidden too long behind the perceived piousness of the biased clergy.
This doesn't mean that the mages will suddenly be atheist but instead that they will be able to practice their faith (which calls for mages to actively serve man) with out being impeded by a chantry that unjustly persecutes them.
I suspect that you're going to run into a chicken-and-egg problem there, because the Chantry is not the only religion that is institutionally suspicious of mage power and worried about abominations. The Qunari have even more draconian practices aimed at suppressing the same (perceived?) dangers. That, to me, says that the religious attitudes about the safety or lack thereof of magic primarily reflect popular "mundane" opinion, rather than the other way around.
More problematically, your argument isn't an argument for the withdrawal of a religious institution from a secular sphere. Rather, it looks like an effort to redefine popular understanding of the religious institution's reason for involvement, and change the mechanics of that involvement, rather than remove it entirely. You don't really have a whole lot of reasons for proposing this thing, but the only one that makes sense and that would potentially mean anything to Thedosians is the first one, where you appeal to the Chant itself. If your reason for mage freedom is "because the Chant says so" then you really haven't taken the Chantry out of supposedly secular affairs, have you?
There's also no convincing description of precisely why the matter is a secular one as opposed to a religious one. In fact, if any one solution is to be imposed, regardless of what it actually is, Chantry support and participation will be necessary, rather than excluded, because it is the only institution that actually covers all Thedas. It is
both a religious organization
and a secular one of immense power. Condemning it for failing to adhere to some anachronistic western Enlightenment concept of separate religious authorities badly misses the point.