If that being of light is Andrastre then Bioware have flat out lied previously, because if we have to become the Herald of Andrastre or something similar how the heck can we 'doubt' or oppose the biggest mortal evil in Thedas? The chantry. Seriously every time we have contact with them or their ideology it is either incompetent or actively malevolent, leading me to believe it's obfuscating stupidity.
Not that I think the being of light *is* Andraste, but if it is, unless she starts speaking in blatant truths, there's still plenty to doubt about the Chantry. Not going to draw real world parallels, but just for starters....which Chantry tradition is correct? The Tevinter Chantry or the Orlasian? What is the truth of Maferath's betrayal? Of Hessarian's mercy?
She was a historical figure, around whom a religion was posthumously formed. Her rebellion may have been purely political, with religious overtones added after her death. The foundation of the Chantry upon her legend, may have been pure expediency. What if she truly was nothing more than a powerful mage? Andraste is nebulous, the pure truths about her mostly forgotten or exaggerated by legend. If she were included in the game, it in no way means that the Chantry becomes beyond reproach. Indeed, if Andraste *were* to appear, it could destroy everything the organization has built.