It's your right to interpret it as bad, of course, but to answer a question like 'what is the Maker' and such things in a game would require either to make him an evil force or a good one. Keeping that question unanswered leaves people able to stick with their interpretations whether that be good, bad, or neutral.
I, personally, see the Chantry is a problem as are the interpretations of the chant of light, but spirituality and the belief in the Maker is not necessarily bad. Leliana has a rather nice interpretation of her faith that differs from what the Chantry teachers for example.
There's also so many theories they'd have to pick one, if they haven't decided on something already behind the scenes.
I know I read that Gaider doesn't like it when worlds, like Forgotten Realms, have irrefutable evidence of the existance of gods.
Personally, I like worlds that do. But this series is similar to real world things, with their faith and their theories, and it's tied too much into the world in such a way that it defines alot of the world. It'd shake up things pretty big and get rid of one of the things that defines the series, I'd think. If they did decide to answer anything big, I bet it wouldn't be in the current age.