Well, the Dwarves already present a significant problem for the chantry. The whole idea of the Maker is that the Fade is his domain, and that it is where we go when we die.
Well, Dwarves don't. They aren't connected to the fade, which is why they are resistant to magic. It takes a large amount of magic to bring them there, it seems, like with Varric in DA2 and Dwarves/the Warden in DA:O.
So where do Dwarves go? Did the maker make THEM? Why should they care?
Anyway,
I don't think the Maker will be corrupt. Why? Because he's already painted a far cry from the normal god-figure. He is said to have abandoned his creations, which suggests that he isn't omni-benevolent. It's been suggested that he couldn't save Andraste (or wouldn't), so he might not be omnipotent. And I haven't really seen anything to suggest he's Omniscient.
He's also depicted as being somewhat vain, among other things.
With a diety that's already so far from being pure and good, I don't see any reason for him to be corrupt. I mean, say he created the Darkspawn to teach the world a lesson or for revenge. You don't really need to redefine the Maker at all to make that work.
I'm gonna guess it'll work something like this:
The Maker is the strongest of a hierarchy of gods.
The elven gods are next. I'm going to guess that they are actually spirits that the maker created, but who grew powerful enough that he couldn't reliably control them.
The old gods are like the elven gods, but instead of being fade spirits, they were dragons in the real world. Perhaps they were created by the maker, but made powerful by the elven gods (but managed to usurp power from them by making deals with mortals).
Darkspawn are probably a byproduct of a war between these three factions. Maybe the actual conflict corrupted the mortals that got caught in it, and the enmity turned them into monsters.