It overlaps somewhat with something I was just recently thinking with regards to Dragon Age: Origins. Faith is central to the plot in Dragon Age as nearly every character will go through dialogue at some point working out their relationship to the Divine: a natural consequence I think of the in-game events like our frequent trips into the Fade (the game's version of the netherworld). The different reactions characters have to the Maker is pretty interesting; Leliana is especially devout, but flirts with heresy because she claims to have theophonic visions; Alistair was training to be an inquisitor but is ambivalent about the Maker.

Her reaction to Leliana's probing about her beliefs is interesting because, general arguments in favor of atheism notwithstanding, her own experience, even in the game as we play, would seem to undercut her position in some ways. She is a swamp witch and her mother is either a demon or a dragon, which means she works in the supernatural even if she rejects a "primitive fear of the moon." She has been into the Fade many times and seen the Black City in the distance: the place that was once Heaven. We see her speak to more than one demon and the demons seem to believe in the Maker.
None of this, of course, really speaks to the actual existence of the Maker, but it does provide a unique paradigm on the nature of belief. If Morrigan is right and the Maker is a lie, then the world as it exists in the game is not undone really but it leaves some important questions. What is the relationship between "natural" and "supernatural" without a deity implied? What would make supernatural creatures like demons and dragons believe in the Maker? Do spirits have faith? And in this paradigm where there is no deity what is the meaning of the Black City: the one artifact that would seem to demonstrate beyond doubt the existence of a Maker?
Of course, this all skips past a pretty important question: why is Morrigan the only atheist?
This overlaps with a discussion I plan to have in Warhammer 40K because theism and atheism are highly troubled categories there. The "Horus Heresy" books are particularly illuminating on this point because they cover the central event of the W40K universe: the Horus Heresy: the time when half of the legions of the Emperor betrayed him and started worshiping Dark Gods. In Fulgrim we read the story of the eponymous Fulgrim, exalted leader of The Emperor's Children space marine legion. The book covers some history of the legion, but focuses mainly on Fulgrim's fall and the corruption of himself and his officers by a demon of pleasure. I think Fulgrim really highlights the theist/atheist relationship in W40K - moreso than, say, A Thousand Sons or Horus Rising (though I should probably read False Gods to get a better idea) - because the consequences of both are highlighted for the Emperor's Children legion.
As a bit of background, in the 31st millennium the Imperium of Man is ruled by the Immortal Emperor and protected/expanded by his genetically engineered super soldiers the space marines. Man travels the galaxy by jumping through The Warp, a plane of psychic energy. Part of the expansion of the Imperium is the spreading of Imperial Truth - a strictly atheist doctrine that teaches the glories of a unified mankind through knowledge and technology* - through propaganda and missionary-like figures called iterators. The consequence of indoctrination in the Imperial Truth for Fulgrim is that when he is warned by a group of aliens about the coming treachery against the Emperor and the great war he rejects the idea entirely because he rejects the idea of demons. The aliens are baffled that humans can travel the Warp - the place where gods and demons come from - without believing in them. This non-belief sets up Fulgrim for his fall as he becomes enraptured and finally possessed by a demon.
Part of the consequence in-universe for this Evangelical Atheism is that it turns inside out because of the betrayal of half the space marines. The Imperium goes from strictly atheist to zealously religious in a hundred years, setting up a cult of the Savior Emperor as well as a multitude of religious military orders and the Inquisition.
It's the demons' relationship with the Warp and the knowledge they have - and, in some respect, the knowledge the Emperor has - of the Warp that raises similar questions to those raised by Dragon Age. There is no God implied in W40K, so again there is the question of the relationship between natural and supernatural with no deity; is a "superstitious" belief more palatable without the idea of a deity? One reads in the Horus Heresy books that part of the reason the traitor marines fall is because they reject the word "demon" as applied to warp creatures, though they know of the existence of creatures in the Warp. I get the sense, though, that this is a distinction without a difference and that the space marines really reject the word only insomuch as it has religious meaning. The need to avoid the words "spirit" or "demon" does, however, cause them to go to some length to downplay possible threats from the Warp. Is religious terminology really that important, though? What W40K implies is that it is religious terminology, or the phobia about religious thinking through that language, that is dangerous to human progress and unity. Yet in-universe the terminology is describing a real thing, something that eventually can be described by an interesting blend of science and religion (the Warp has natural laws, but creatures there are fueled by psychic emanations, i.e. faith). It is a "rose by any other name" problem. Could the use of religious terminology close the door on scientific investigation, even if describing the real?
My dissertation will probably focus more on the idea of W40K as utopia/dystopia so the theis/atheist conflict will arise mostly through a discussion of this universe as a possible model for a relationship between science and faith. The problem I see though is a postmodern one: there is no clear indication of moral value in science or in faith here. Horrible things happen because of people having no faith, but horrible things also happen because people have faith. Likewise, horrible things happen to advance science while horrible things happen in scientific ignorance. That seems to preclude the typical didactic tut-tutting in some sci-fi about religious "fanaticism" or science gone "too far!" One message seems to be that there is no binary between science and faith and that the relationship is a complex and sometimes complimentary one.
The bigger message though is that humans can be horrible and even in 30-40 thousand years we'll still be acting horribly! That's actually a rather refreshing message, I think: a final and complete rejection of this 19th century idea (owing to the Enlightenment, Orientalism, and Marxism) that somehow scientific progress goes hand in hand with moral progress.
*There is also an intense xenophobia as part of Imperial Truth that gets held over into the time of the God Emperor, but that interesting tidbit is for another time.