As someone who owns a complete Mythos CCG collection, far too many Arkham Horror expansions, and is a bit of a Dominion fiend, this sounds totally cool.
Kyle: Given what you said, would you still recommend it as a 2-player game? I'd be playing mostly with my wife who doesn't care at all for direct conflict mechanics.
I don't know if I'd recommend it solely as a two-player game - I think you'd be missing out on a lot of the potential of the game, and you wouldn't get to fully exercise a lot of the features of the game (such as blocking discs) that are more useful when you're working with or against multiple players.
Although even with two players, it's not exactly a direct conflict game - since your "side" is determined randomly at the start of the game, you could both be Loyalists or Restorationists, meaning you'd both have the same goals of either assassinating Old Ones or protecting them, but you'd just be racing for points, in terms of assassinations/saves conducted, cities controlled, or certain victory point card effects. So you'd kind of be on the same "team" but vying for points. Yes, still "conflict" but with a nice veneer of theme that puts you on the same "team".