That's where it gets confusing. On one hand we have History of the Circle describing mages being oppressed and pushing for independence. On the other hand, we have Nevarran Accord, based mostly on David Gaider's interviews and comments, which claims that "After the first Blight, the Chantry recognized the mages’ value in helping protect humanity and so sought a better solution". I think it would've been royally stupid to force mages to light candles after all the spells they unleashed upon the darkspawn in the First Blight. It is also weird because the Circles in Tevinter are prestigious academic institutions and not places of seclusion for mages.
As for Andraste herself, her views might've been quite different from that of even the early Chantry. According to the World of Thedas, Prima Guide and Sister Justine:
"A cult known as the Cult of the Maker grew out of the legend of Andraste's martrydom. The cult had no central leadership and its followers were oppressed. The clerics had to hide their lore from Tevinter magisters by way of ciphers and encoded scrolls. In -130 Ancient, cult practitioners organized Andraste's teachings into hymns, creating the Chant of Light and the cult popularity spread. The cult remained fragmented until it was formalized into the Chantry by Kordillus Drakon, the first Emperor of the newly formed Orlesian Empire".
After all that time, the views and texts could've been changed a lot of times. I base my thoughts on the Chant of Light itself, it doesn't condone magic or magic users per se but rather the oppression of magic and its hold over mages' minds.