He lets her go. He lets Amy go. His Amy, the dearest, the most important person in Rory’s life. Amy is and has always been what Rory values the most. Not even his own life means this much. He would trade it, he did trade it, for her life, her safety, her well-being instantly. When she suffers, when she’s endangered, when she’s in need, insecure or terrified, Rory will do everything in his will to save her from harm or take it all on himself if he cannot prevent it. And here she is, in pain, scared, confused, they both have no idea what is going on, what is true and what is not anymore. And the Doctor orders him to leave her. To let her go. God knows where, what will happen to her, how long they will be separated, if they ever see each other again. Doctor orders him to leave her, to let her go, though Rory swore to himself, to her, in his heart since forever and in his wedding vows he will keep her safe and protected, always. Always by her side, always having her back. You and me, always.
And it is killing him, breaking the vows, hurting her with his betrayal, because that’s what is.
Yet he does let her go, though she pleads for him not to, though she clings to him like he’s the only confirmation of truth and safety. The way she always does. She shakes her head in disbelief and despair and yet Rory’s body moves on its own.
Because the Doctor asked, because he ordered. And Doctor’s word, his request, his disposition means more than Amy’s fear and confusion. In his trust and devotion to the Doctor, Rory is willing to risk everything he pleaded to keep: Amy’s safety, him being by her side no matter what. Deep down inside he is certain (or he believes, but he believes so much that it equals with knowing for sure) that Doctor knows the answers to all the doubts, he has always known, and he has always managed to save them by the end of the day. And so he will this time, as well.
The moment he stepped on board of the TARDIS, the moment he didn’t try to force Amy to go back with him, it all proves Rory trusts the Doctor with Amy’s life, which by default means he trusts him with his own life. And it’s all the more valuable, as it’s not dictated by hero worship and false idealisation. This trust in the Doctor has been many times verified by Rory’s down-to -earth approach, his scepticism, his distance balanced with reason. Rory does not follow Doctor blindly. He follows him because he saw with his very eyes Doctor’s devotion to them, he felt all the Doctor’s care, love and protection. Doctor is not an invincible hero, magical figurine with otherworldly powers in Rory’s mind. He is a loyal friend, willing to do anything to protect them just as they are in return. Doctor is a family you trust completely not because they showed you you can, but because there’s intimate, deep bond formed between you, out of so much mutual experience you had been through together.
Rory does trust him completely and Rory does let her go. Though it feels like betrayal, with Amy terrified, looking at him with hurt and accusation, making him suffer her pain, making him hesitate, but in the end doing what Doctor orders he must. Despite of Doctor being harsh, cruel and definite, offering little or no explanation. Though it costs Rory so much effort, still it stems from equal amount of faith. Because it’s the Doctor. Because he’s a friend. He’s a family.
This is his ultimate testimony of faith and trust in the Doctor. Even grander than Rory’s sacrifice in “Cold Blood”. This time it’s Amy’s life at stake, something much more valuable to Rory than his own life he gave to save the Doctor then.
This is how much Rory trusts the Doctor.