That's what I thought you suggested. Sounds interesting, but the first thing I thought of was the Indoctrination Theory of Mass Effect 3. And it's not a good thing for one big reason:
The indoctrination theory was some sort of alternative explanation for the bad writing bits of Mass Effect 3 (I doubt anyone would have thought of this theory if the game's story was able to deliver a satisfying conclusion). I just don't think Larian are clever enough to pull off something like that. The good news is that we don't know yet either way.
If I may pitch in, with all the datamined content discoveries so far the plot post Act 1 looks more like a do-over of DOS2 than anything as lofty as this. The Absolute is just Lucian again, the gods are tackling this new threat by sending their champions after you ("locked" companions stay loyal to you and everyone else becomes a conduit for their god) etc. etc. You even get shipwrecked and saved by a god AGAIN.