It's those issues that tend to color how some people look at the Chantry, whether or not the person is religious. It's not as though the Chantry is an actual religious organization, after all; it's a fictitious group that is involved in some questionable behavior.
Speaking strictly for myself, I've never been able to understand why a mage would even follow the Andrastian faith, given what they preach about mages and magic.
However, I doubt the Cult of the Elder One will be much better.
Laidlaw's tweet does make me believe that there will be an option to rebuke association with the Andrastian faith, for the Dalish and Vashoth protagonist, and hopefully for a Dwarven main character as well.
Well it's pretty clear that Andrastian faith is to the world of Thedas what Christianity is to ours, the connotations are there and anyone regardless of belief can grasp that. It's interesting because the God of the Bible is a god outside the world that created the world while other gods are just idols of this world made by men for men, <- this has been used by Bioware for Dragon Age, you have lots of different gods and pagan beliefs in Thedas with people worshipping the old gods (seven dragons) and elven gods and a pantheon of gods of the sky and wind and earth, this gods are ultimately gods of the world, while the Maker is well... the Maker, so he isn't bound by the world.
And I'm not saying The Maker is a carbon copy of the God of the Bible, first because the world of Thedas is much more different from ours and second because the Maker seems to have just said "ok screw it, I'm out of here" or at least he is very apathetic about the world, while the God of the Bible is more personal and interacts with mankind to save it throughout all history.
So yeah, I can see references to our world and how people could see the Chantry as the Church of Christianity. As a christian myself I guess I could psychologically speaking perceive the Chantry or the Maker with friendlier eyes because they are in DA world what christianity and God are to our real world, while an atheist could see the chantry and its faith with more reservations if in his real life he perceives christianity or God (or any other faith) the same way.
But ultimately the religions of Dragon Age are fake and made by writers in a studio. We shouldn't see it in any other way. The similarities are just that, similarities.
Now about the Andrastian faith what it says is that magic exists to serve man and never to rule over him - This I like. It's a very moral statement in my opinion, if you have power you have to use it with responsibility (this notion wasn't invented with spiderman).
Another matter is how this statement is exercised. The white chantry imprisons mages and has them under constant surveillance while the Black chantry in Tevinter says that this statement doesn't ban mages from ruling and just means not using blood magic (and they still use it lol)
Many people have a hard time separating the tenets of a faith from its practice by men. Someone can proclaim that he/she is this or that and then contradict what his faith says by doing the opposite out of ignorance, stupidity or for the lulz.
So lore speaking I can see a mage that has faith in the Maker and at the same time wants to reform the chantry to adjust its practices better to what the faith in Andraste and the Maker says.