I like you always know how to spin a theory and have it seem plausible with a bit of dramitic flare
I like drama. But really, not even the Old Gods could resist trying to take whatever they thought was in that City, so how could the Elder One just ignore it?
Inquisition is a story about something trying to make itself God, and the last time we had that it involved the City. There's not likely to be a better story for the subject matter to be explored. Leaked Achievements suggested that Corypheus is coming back, and he's probably had enough time to settle his head and get everything screwed in right so as to be more lucid when we speak to him next.
All of this meaning that we may be able to ask him what the hell happened with the City and how he got there. He's the perfect source of Black City exposition, and since he's likely not living past Inquisition, we won't get another chance to talk with him about the matter.
Now, if I may get into empty speculation, I did have a recent thought on how the Elder One might meet his demise. It's a bit of a foolish thought, but it might be fitting if the final confrontation took place in the Black City itself, perhaps protected by his magic green hand. I imagine that the city itself would be eerily beautiful and filled with mysterious music and perhaps a few grotesque oddities.
But I digress. It might be fitting, at the moment the Elder One appears triumphant, for a mysterious something to reach out from the heart of the city and tear him apart or pull him into an abyss. Something of that sort. With that mysterious something than proceeding to go after you, maybe as that mysterious green fade lady reappears and tells you to run while she stays behind and starts singing as the presence grows closer and the whole city starts to freak out.
This should all preferably happen in the most horrifying manner possible, with the music of the city growing ever more threatening, frantic, and just generally terrifying and wrong as it all happens. You never see what it is that's in the city, except maybe enough of a vague silhouette to know that you don't really want to see it.
Later, you wake up without your magic green hand, with all of the rifts sealed and you back on Thedas. Everyone is sure you saved them all, but they want to ask you what you saw in the city and how it all went down.
So, you have some of your last remaining dialogue options. You can tell the truth, say nothing at all, or lie. You can say you saw nothing, that you handled everything yourself. or that you saw something good and beautiful. Or you could tell them all what you really saw...
Whatever you say, it will have some impact on Chantry beliefs in the next games, even if it isn't obvious. There wouldn't be anything proving the existence of the Maker per se, only a horrifying Eldritch Abomination of tremendous power, kept pacified by the singing of a mysterious woman in the heart of the Black City. Sort of like Azathoth and his flute players.
Of course, the Maker was supposed to have left the city, wasn't he? Ah well.
EDIT: In case you don't know who Azathoth is: http://en.wikipedia.org/wiki/Azathoth