One of the things that is never properly addressed is the Chantry as a political institution. The southern Chantry was the brainchild of Drakon. It was his deliberate intention to spread the faith by force if necessary, and conveniently extend the range of his empire at the same time. Even his friend Ameridan could see that Drakon was intending to "simplify things" and this was going to cause problems for people like himself. His compatriots in the Dales were a bit more astute and saw Drakon, his Empire and his Chantry as a second Tevinter. Hence why when they finally went to war they headed for the seat of power in Val Royeaux. In a way it is a pity they didn't succeed. Still the Chantry is not promoting the teaching of Andraste, just Drakon's interpretation of it. There were apparently many different sects devoted to Andraste prior to his Chantry, which he wiped out in his efforts to simplify things. According to the World of Thedas 1, the chief tenants of the faith are:
1.. Magic is a corrupting influence in the world.
2. Humankind's sin of pride destroyed the Golden city. (mages again)
3. Andraste was the bride of the Maker
4. Humankind has sinned and must seek penance to earn the Maker's forgiveness. When all people unite to praise the Maker, he will return and make the world a paradise.
Notice that the number one belief in Chantry doctrine is that magic is corrupting. Compare this to what the Chant claims Andraste actually said:
"Magic exists to serve man, and never to rule over him. Foul and corrupt are they who have taken his gift and used it against his children."
The Chantry doctrine has totally twisted a core part of the teaching of Andraste which is that magic is a gift of the Maker to be used for the benefit of mankind and it is only those who have abused this gift and used it to harm rather than serve the needs of the community who are corrupt.
Whether the Templars were universally abusive or not, this basic teaching of the Chantry has influenced the way mages have been treated in the south ever since. Remember even back in DAO we were told that the Chantry selected its Templars more for their religious fervour than their moral fibre. It is easy to see how so long as an abusive Templar yells "praise the Maker" at frequent intervals he can get away with just about anything.
The ironic part is that the first official cult of Andraste was founded in Tevinter by Hessarian. He set up the first Circles of Magi for the education of mages and study of magic on the sites of the old god temples. It was his intention that thereby all mages would be properly be prepared for a lifetime of public service. Hessarian, a mage, was both Archon and Chief Priest of Andraste. He allowed Soporati into the ranks of the clergy and soon they achieved high-ranking positions both there and in the Magisterium. However, surviving Altus from his purge of their numbers simply converted to the faith and from there found their way back into the chief positions of power. At that time it would seem that both men and women had equal chance of promotion. It seems to me that the rise back to power of the Altus had less to do with their magical ability and more to do with the fact that they were historically the aristocracy. Still, apparently things went along just fine in the north for some 150 years, on the face of it pretty much in keeping with what Andraste taught, while the south was still a bunch of fragmented warring tribes with numerous cults to Andraste, the Maker and other gods.
It was only when Tevinter approached Drakon's Chantry for recognition of their mutual faith that things started to go wrong. To be honest I'm surprised that Tevinter even bothered but they did and made certain concessions to the Chantry in order to achieve this. Most notably they reduced the Archon's role in the Tevinter church and authority over the faith was transferred to the Grand Clerics, just like the south. However, everything else was kept as previously and yet the Chantry in the south seemed to think they had monopoly over the interpretation of the faith and that Tevinter was the one who had altered the Chant of Light to reflect their interpretation of it. It is noticeable that it was only after the state of Tevinter had been repulsed from the Marcher States after doing a bit of power building by an Exalted March declared by the south that the story about the Ancient Magisters being responsible for the Blight started being promoted by Orlais. Strangely enough the main text which points the finger at them was the one produced by Hessarian, that was ultimately rejected by the then southern Divine as political propaganda, but then clearly reinstated for political reasons. It is noticeable that in the basic doctrine of faith of the southern Chantry and in the Chant itself, the finger of blame for the Blights is pointed to mankind as a whole.
Anyway, my point is that the immediate reaction to Andraste's crusade was not to immediately rail against magic. This is why members of the early Inquisition and its last leader could be a mage. It is recorded that they only went after mages who were a danger to the community and could just as often be found protecting them from unjust accusations. The Rite of Tranquility was clearly originally intended as a protection against possession and mind control, useful when going up against maleficarum using blood magic for that purpose and stray demons. The reason they were disliked and their reputation subsequently vilified was that they treated everyone equally, including the nobility, when dispensing justice, something the later Chantry has consistently failed to do. It was the worst thing that could have happened for the Inquisition to have gone from being an independent organisation to a stooge of the Chantry, which is why I prefer to disband the second Inquisition rather than place it under the Chantry once more. When I disbanded the Templars and placed them under the Inquisition, I felt I was really just reversing history (although my true satisfaction only came after Jaws of Hakkon). Whatever ultimately went wrong up in Tevinter, I believe it could have been very different if the southern Chantry hadn't got involved with their set up and if the south hadn't shown themselves to be so fervently anti-mage and anti-magic.