To me, Chuck is a pretty safe way of understanding the world. He's a good guy, but he's not all powerful. He can fix some things, but he can't really fix everything. He's also realized, on some level, that he shouldn't fix everything. So he watches us from afar, either doing a little here and there or simply leaving us be. .
I think this makes sense up to a point, but "Moriah" points out that Chuck's unwillingness to interfere looks less like respect for free will and more like a decision to put Sam and Dean in harm's way at all times for reasons that "Moriah" finally revealed.
From a real-world standpoint, nine seasons of Sam and Dean enjoying peaceful semi-retirement was never on the table. But from an in-universe standpoint, "Moriah" observes that Chuck has by passivity forced Sam and Dean to serve as Earth's protectors despite continual loss and suffering for them.
Season 11's "Don't Call Me Shurley" had Chuck putting the blame for the recent run of threats on Sam refusing to lose Dean to demonic conversion. But in Seasons 12 - 13, Lucifer's return and the alternate universe situation were due to Chuck once again abandoning his son and a "failed draft," yet Chuck did not return to help.
By Season 12, any benevolent employer in Chuck's position would have put Sam and Dean on vacation and found some new hires to act as Earth's divine defense division. It didn't have to always be Sam and Dean facing every conflict between heaven and hell. They'd done their part and more, it could have been someone else's turn to take up the mantle. It could have been Charlie. It could have been Jodi Mills, Donna Hanscum, Kaia Nieves, Claire Novak, Patience Turner, Alex Jones.
But Chuck allowed WAYWARD SISTERS to fail. What kind of God would fail to get WAYWARD SISTERS picked up? Why did Chuck always want it to be Sam and Dean?
CHUCK: "I built the sandbox -- you play in it. And you're my favorite show."
SAM: "But why, when the chips are down, when the world is -- is failing, why does it always have to be on us?"
CHUCK: "Because you're my guys."
Chuck says he's granting humans their free will, but then the episode points out that Chuck always puts the consequences of his supposed non-interference entirely upon Sam and Dean. Why is Chuck allowing two exhausted, traumatized, burnt-out employees to carry on performing their duties with steadily diminishing efficacy and ability? As if to answer this, Sam observes Chuck taking pleasure at the sight of Dean's agony.
SAM: "You're enjoying this!"
And when Dean refuses to follow Chuck's plot direction, Chuck suddenly gets upset.
CHUCK: "This isn't how the story is supposed to end. The story? Look -- it -- the -- the -- the gathering storm, the gun, the -- the father killing his own son. This is Abraham and Isaac. This is epic!"
DEAN: "Wait. What are you saying?"
SAM: "He's saying he's been playing us."
"Moriah" completely overturns the Chuck character as we know him. But "Moriah" makes a very clear point: Sam and Dean have been forced to manage Chuck's responsibilities since Seasons 6 - 14 when their roles should have been over by the Season 5 finale.
Part of this is, I think, a wry commentary on and from the writers who have, for nine seasons, had to come up with new threats and new suffering. The original authorial intention for Chuck was to make him a warm and loving father figure who represented the writers and their affection for the characters. Chuck allowing free will and acting indirectly throughout Seasons 1 -5 to maneuver Sam and Dean into averting the Apocalypse without overruling individual choice was heroic. Chuck acting indirectly throughout Seasons 6 -14 to keep Sam and Dean in the line of fire for nine years after the original crisis, however, is manipulative and cruel.
SAM: "This whole time. Our entire lives. Mom, Dad -- everything. This is all you because you wrote it all, right? Because what? Because we're your favorite show? Because we're part of your story?"
DEAN: "The Apocalypse, the first go-around, with Lucifer and Michael -- you knew everything that was going on, so why the games, Chuck, huh? Why don't you just snap your fingers and end it?"
SAM: "And every other bad thing we've been killing, been dying over -- where were you? Just sitting back and watching us suffer so we can do this over and over and over again -- fighting, losing people we love? When does it end?"
CHUCK: "Fine! That's the way you want it? Story's over. Welcome to the end."
Unlike the writers, Chuck is not required to deliver 20 - 22 episodes a year, not obliged to make Padelecki and Ackles' characters the center of a TV show and not bound to create a world-ending situation on an annual basis. The only explanation for why Chuck would continue to do it is because it amuses and entertains him to watch Sam and Dean suffer.
It doesn't fit the charming, grounded, silly character that Rob Benedict developed and played. This is a sociopathic puppetmaster, not the well-meaning observer who turned Benedict from a middle-aged, over-the-hill actor and part-time musician into an idol of positive masculinity and unthreatening appeal for a legion of fans.
This is a complete reversal to one of SUPERNATURAL's greatest creations. It's a shocking and painful betrayal. But it seems to me like the inescapable result of extending the lifespan of the series.