I skipped pages 3 - 5 of this thread in my eagerness to reply, so forgive me in advance if I missed something which was already said.
I love to imagine Leliana as a spy in Origins! The Seeker's Circle amulet gives a +1 bonus to cunning and a +10 to mental resistance (Origins is open in another window on my machine right now, so I just checked), which seems pretty agent-of-the-divine to me. Not something your typical lay sister (or, as Sten puts it, "houseguest" of the chantry) would likely need.
[Beware spoilers out the wazoo, for dlc, expansion, books, ][, and the absurd narrative in my brain.]
Leliana's Song does show us that she knows the Divine, and that the Divine has taken a strong interest in her. Leliana also says (in Origins) that the other chantry folks called her beliefs about the maker blasphemous, which I think wouldn't be tolerated for long were she a regular, ordinary old blasphemer (unbacked by the Divine/someone high up).
From Return to Ostagar, we know that Cailan had corresponded with the Empress of Orlais about assistance in advance of the Warden's recruitment. Lothering sits right by Ostagar, so why not park an agent there for a while? Someone above said she could be an inactive agent; that seems plausible. We also know that the Orlesian Grey Wardens were aware of the blight; they'd probably known at least as long as the Ferelden GWs about the upsurgence of darkspawn and their location.
From the books (more specifically, from The Calling) we know that some Orlesians (high ranking suckers) were in cahoots with the Architect, who may or may not have survived Awakenings, to undermine Ferelden.
So what if, and here beware massively absurd speculation, what if the Orlesians actually knew when and where the blight was going to go down, possibly even years before it did? What if the Divine and the Empress are at odds? What if Orlais and the sentient 'spawn have an alliance? What if Kirkwall's demon troubles (cue Legacy) are darkspawn instigated (Corypheous--sp?)? It could be a nice one-two; undercut Fereldan with the Blight, stir up trouble, sucker-punch Kirkwall and cause civil war in the Free Marches. Maybe the Divine knows what the Empress is up to with the likes of the Archi and Coryphi and is opposed? Maybe there's another assault planned on the Maker's former abode, his works, and instead of Tevinter, it's being led this time by Orlais?
Plus, mix in some Band of Three, a dash of Lyrium Idol/Primeval Thaig, and The Stone Is Alive (Nexus Golem) utterances for extra flavor! Sprinkle liberally with Flemeth, and season to taste with Old God Baby sauce.
My ultimate point being: Leliana could so totally have been a spy right from the start.
Phew! *removes pyramidal-shaped tin-foil wild-theory-intensifying hat and resumes playing Origins*