I don’t know if they indicate outright REBELLION in Cas all along, but more the ‘wrong’ way of thinking. More examples of him showing ‘too much heart.’
Like, I’m imaging not that he refused to take part in passover as a strong stance against Heaven, but more like he was too HORRIFIED and simply COULDN’T DO IT. I’m imagining him shaking and crying. Maybe standing over a child in bed with a knife at his side or behind his back (like when he tried to kill Jesse), trying to psyche himself up, then teleporting outside, leading back against the wall of the house and sliding to the ground where he hugs his knees to his chest and buries his face in his folded arms.
Which is where Balthazar finds him later, his own sword stained with blood. And he starts tugging Cas’ arm, telling Cas he has to do it, it’s an order. But Cas doesn’t respond. So Balthazar suggests he does it and they tell Anna it was Cas, but Cas leaps to his feet when Balthazar moves to enter the hut and holds him back, pleading - ‘no, Balthazar, you can’t, he’s just a child!’ And Zachariah finds them fighting, pulls them apart and flies in to kill the child himself.
When he comes back out he looks at Cas sternly - ‘is there is problem, Castiel?’ Cas just swallows and shakes his head, and Balthazar tries to cover the show of weakness by speaking for him - ‘no, Sir, no problem, it was my fault, Sir, I interrupted.’ But Zachariah can see the pain on Cas’ face. He’s seen it there before. He calls Naomi the moment he returns to Heaven.