I think that is were things get...iffy. And more philosophical than factual perhaps.
Specifically, there is a difference between faith and belief. And again between faith and religion. And again between faith and or religion and the specific actions, beliefs and rules accorded due to the above.
What if you are full of crap? What if NONE of it is accurate, at all? Will that change a persons actions? Should it? What if no-one is full of crap? What if every religion at its core held its own kaleidoscopic view of the same eternal truth? What would change? Everything? nothing?
We become concerned usually when there is inner motivation for others believing as we do. And usually, at some point in history, that concern started a seed in order to create order amongst the masses. It was probably very effective to do so. TV and media is used for the same purposes now actually. It doesn't make it a "religion" but "back when" organized religion was probably the easiest method of reaching the people; today, it's the media.
Need a war? God on your side will help motivate/protect etc. Everyone wants to be "special" so deem yourselves the chosen of your particular god and grab a sword. It makes it more ok to fight for the powers that be. Sometimes, loyalty to your flag, your country or people is the motivational force. It harnesses that same energy though.
Does this fact take away the potential good side of faith? I can see how, unless you are able to step very far back from the emotional center of the picture, that it would be very very easy. For people who hold faith very dear to themselves, they think of it as their "compass", their "core" and their "center". Thus, it would be easy for an action to feel like your very *core* is threatened when it is faced with differences/opposition. Faith is a positive thing in many peoples lives. The issue is not with faith of any flavour itself but with attachment: anything that causes us great emotional attachment is power and weakness in one, power that can be utilized and twisted and exploited. That is an issue of power and emotional attachment, not necessarily faith itself.
The truly dark use this as the main motivation to boost their own political power plays, because it can be just SO effective. But it's a powder keg. Best to have someone else carry it. 
The games depiction *so far* is a bit of a caricature, but at least it is interesting. My fem hum inq just tried to create order, giving no-one too much power. Naturally, it didn't go well. LOL I havent tried to play it as a person with absolutely NO faith yet (but will, maybe next playthough) so not sure how well the game allows it. It doesn't do "Check my dalish gods" very well. Maybe just bugs though.
I get the impression that this was the swan song of the chantry battles in DA though. It feels almost all played out now.
I feel like I have to get people back on track somehow.. To find something truly worth believing in. But what if I'm full of crap too?