For God's job to be taken is a concept that not even Dean Winchester can wrap his head around easily. For angels to accept that Cas is their God is another matter all together. It's a strange idea that should never come to pass.
And God knows that.
No one knows where the Big Guy is, but he knows where everyone else is. He knows what everyone is doing, even if you are monster or demon. The one being that has caught his most attention is his quiet naïve son, Castiel. Cas always obeyed, always fell in line with what God wanted. He followed the script to the very letter.
That's why when Cas sided with the Winchesters—and in a broader sense, the human race—God was extremely proud. When he watched Cas throw the flaming Molotov cocktail of holy oil at Michael, slowing down the fight for maybe a minute or two, he recognized that Castiel, in that moment, was the only angel that had grasped the idea of freedom. He saw that Cas wanted it for everyone.
Then Lucifer killed his little brother, ripping apart his body with only a wave of his hand. But God saved him. He saved his son, because he wanted his son to teach his beliefs to all of God's other children. He wanted them to live like the humans—free to make a choice without someone else telling them what to do or how to do it.
God watched Cas return to heaven, standing up to Raphael, telling his older brother that the Apocalypse should not happen. He also watched yet another archangel hurt Castiel, making him bleed in the home that God created to be a realm of only peace and love.
He watched Cas make the deal with Crowley. He watched Cas lie straight to the faces of his closest friends, through voice and action. He watched it all. And even as all-knowing as he is, the actions of Cas actually scared God. He did not want to watch the only angel that ever turned away from the original script to take his free will and abuse it.
So, when Cas finally started praying to his father, God listened more intently than he had to anyone in a very long time. He listened to Cas confess everything he had done in the past two years, even if he had seen it all. He could hear the pain in Cas' voice as he recalled being trapped by the Winchesters and Bobby with holy oil and having to look at his friends and tell them the truth: he was working with the King of Hell to open purgatory.
Then God heard the most powerful words of all come out of Castiel's mouth; powerful because they brought relief to God:
"I'm asking you, Father, one last time. Am I doing the right thing? Am I on the right path? You have to tell me, you have to give me a sign. Give me a sign. Because if you don't, I'm gonna do whatever I must."
Cas was uncertain about the path he was walking. However, as relieving as this shred of news was, everything else about Castiel brought pain to God's heart.
Castiel looked as if he was struggling. His voice mirrored his distress. He hated making the Winchesters distrust him. He hated working with Crowley. That's why he was praying to God—he needed to know what to do next.
And God wanted to help. He wanted to walk straight up to his son and tell him what to do. But Cas was not like any other angel—he embraced free will and understood it fully. Cas had free will. God could not touch that.
So he did what Cas did with the Winchesters—he came to his son, but remained invisible, choosing instead to just watch him. God could see the dread is Cas' face when he heard no answer. He watched his son—still so innocent and naïve—hang his head in surrender.
He watched his son visit Crowley almost as much as he visited Dean. And he watched when Castiel didn't visit either and instead appeared outside the house of the Novak Family—the family of Castiel's vessel. He would slump against the wall and take just one moment to let the reality of the situation hit him full force. He would stare off into the night and close his eyes, letting the tears fall. Letting himself feel human for only a moment.
He watched his son take in all the power of the souls. He watched Castiel kill Raphael, something that brought no joy to God. He watched Cas proclaim himself as "Your New God. A better one."
Still, God did not interfere. He didn't want his old job. He wanted to stay in retirement. He told himself this. But he kept watching Castiel. He watched as the Winchesters barely escaped him with their lives. He watched them become fugitives from the wrath of heaven.
And he watched all the horrible things Cas did. For a year, God let it all happen. He didn't do a damn thing.
And then Cas said he would do the one thing that is forbidden. It doesn't matter if you obey God or not. Even Lucifer, the biggest rebel of them all, knew that this is what can NEVER be changed.
Castiel wanted to remove free will from the entire universe.