There are two things I love about this moment.
First of all, Sherlock protects John. By pointing a gun at his head, yes, but think about it. Sherlock’s name is already being dragged through the mud. Scotland Yard already thinks he’s a psychopath and a possible murderer. Even before the Moriarty debacle, his name and reputation were already tarnished with people like Sally Donovan, and it’s only getting worse.
John’s isn’t. The most John gets from outsiders is a bit of confusion. People figure he’s either a bit daft or touched for sticking with Sherlock or that he’s too kind-hearted to leave him because he’s all Sherlock’s got (supposedly). But he isn’t judged or looked at with disdain in the way Sherlock is.
Sherlock obviously knows this and when he finds himself having to drag John into this mess with him, he doesn’t hesitate to protect John’s name. He makes himself look even worse in the eyes of the Yarders by pretending to take John hostage, which also keeps John’s good name somewhat intact (he did just punch the Chief Superintendent, but that’s a far cry from pulling a gun on a bunch of cops and fleeing an arrest).
Second, John completely and unwaveringly trusts Sherlock. Wild, unpredictable, reckless Sherlock who throws himself into danger’s path again and again, points a gun at a crowd of police officers and then turns and points it at John’s head, his finger on the trigger and John doesn’t so much as flinch. In fact, he seems far less uncomfortable with Sherlock pointing a gun at him than with Sherlock pointing a gun at other people, because he knows he’s safe. There are no questions asked and no hesitations. No “Maybe we should think this through,” no “Why are we running when we both know you’re innocent?”, no “Be careful with that deadly weapon you’re waving around”. There’s a “What are we doing?” but it’s spoken more in the tone of “Let me in on your plan so I can work with you” rather than suspicion or apprehension.
Yes, we know that Sherlock would never do anything to seriously hurt John and John knows that, too, but accidents do happen. High stress situations, people panic, get a bit jumpy, fingers slip… But John trusts that Sherlock knows what he’s doing, trusts him not to make a mistake with John’s life in his hands, and trusts that he has a plan and that it’ll work. In all this mess, with Moriarty worming his way into the heads of everyone around them, planting doubts and twisting truths, John still trusts Sherlock wholeheartedly.
Because that’s what John and Sherlock do. They protect each other and they trust each other, no matter what.
/end lyrical waxing.