In a recent article, Rob Benedict talked about the difficulty of bringing his character back. "It’s so self-conscious…" he says. "It’s kind of hard to just have him walk through the door and be like ‘Hey, how’s it going'?"
I don't think it's hard at all! You just have to love Chuck and Rob Benedict enough to be motivated to find the solution. :)
I think Chuck was not meant to be God from the beginning of his story thread. I just can't buy that God would sit alone in a ratty bathrobe and dial up porn while drinking bad whiskey. Yes, he took on a role to hide his true identity from the boys, but when they weren't around, who was he playing for?
Therefore, I think Kripke came up with that very fitting closure to his tenure as showrunner well into the season. It made "early Chuck as God" a little unbelievable, but now it makes bringing Chuck back super easy.
I don't think they have to bring Chuck back as God, or bring the "real" God onto the show at all. So far, God's presence—except for that one episode in the final moments of the Big Battle—has been off screen. He's done incredible things, like bringing Cas back (twice, really, and geez, this is how Cas repays him?!), but all from afar. Gentle nudging of events, not direct interference. Cas isn't the first being to declare himself lord and master, so God really doesn't have to change his behavior. If he wasn't going to jump in to prevent the apocalypse, he's not likely to show up for this poser.
Sam and Dean don't know that Chuck was "God." As far as we've seen, they haven't tried to find or contact him since Sam went into the pit. They can do a quick explainer, of course. Dean saying, "Dude, I tried to call you like fifty times." Or they can just admit to having been so wrapped up in their own issues they didn't think about him.
But what do Sam and Dean think happened to Chuck? (Rhetorical question.) If God only took Chuck's role for a short time, where did Chuck go during that? Maybe he was sleeping some real, awesome, dreamless sleep while God took over his prophet duties. Maybe, when he woke up, he realized he could have his life back. Or actually have a life. He wrote a new book, all his own ideas, and sold it and became a bestseller. In the meantime, he worked in a toilet paper factory (because it takes a long time to get from Page One to NY Times Bestseller list).
Okay, that established, what kind of storyline could draw Chuck back to the screen for us? Throw out some ideas!