It seemed that way from what Dean said earlier about the Collectors' base and such, but it appears he is thinking differently now.
I'm not sure on the 'ordained by God' thing though. There can be different consequences, but in Mass Effect they just tend to look at how a player deals with a situation and then encourage players to follow a set path and keep some sort of consistency in their character. A lot of the 'right' and 'wrong' stuff seems clearer when it's simply viewed as 'optimist' and 'pessimist' but I think there are probably still moments in the game where it gets a little blurry (Legion's loyalty mission perhaps).
Wish I could find the interview, but Muzyka and Zeschuk are clearly aware of their own design goals in Mass Effect. Shepard is a character with a backstory and, in a way, the player is reacting to the narrative (rather than more open decisions) and is being given a lot of control over it rather than developing their own blank character as they did in Dragon Age: Origins.
And just to be clear, I'm not trying to fanboy Mass Effect or anything (honest!), since it is not perfect in utilising a karma meter. It just appears BioWare are not arbitrarily implementing one as some developers might.