There is a half-second before Sherlock pulls the trigger. A half-second in which he looks at John, and nods the tiniest nod, and maybe they've only been (flatmates? Friends?) together for a few months, but John reads an awful lot into that look in what he knows will be the last half-second of his life, which seems to slow into years (and this has happened once before, hasn't it?).
John reads the obvious apology first. And then wonders why it was 'obvious', because Sherlock never apologises for anything. Not even to him, normally, but there it is.
And then it's more than 'I'm sorry for getting us both killed'. John thinks he can see 'I'm sorry setting you on fire that one time', 'I'm sorry for dragging you out at all hours of the night', and maybe even 'I'm sorry I never bought any milk in my entire life, but mostly while I was living with you'. That one might be wishful thinking, though.
There's regret there, as well. John thinks it's important that that's separate from the implied regret of being sorry for something. This is Sherlock feeling sorry for himself, which he also never does. Well, that's a lie, but it's never in the honest way that normal people feel it. He feels sorry for himself when there aren't any gruesome murders for him to solve, but he doesn't actually regret that. For all of his impressive lack of tact, he's doesn't actually want to see anyone die – he's never wanted to see anyone die, and that bit might make him a better man than John, because John has genuinely wanted to end the life of another human being before.
He's done it for Sherlock, after all, and whilst John doesn't doubt that Sherlock has the capacity to kill someone, he's pretty sure he wouldn't do it on purpose. Or at least, not as the motivating factor behind an action. Kill them because he wanted to see how some new and exotic poison worked? Sure. But not because he wanted them dead. He didn't care enough about anyone to want to kill them.
Or maybe he did, because he was about to kill Moriarty – the greatest opponent, as far as John could see, that he'd ever faced. He could let this man go free and never be bored again. So why was he killing him?
For you, a little voice spoke up in his head. He's killing him because he got at you.
Maybe Sherlock isn't so above all this human emotion stuff after all. And that, John realises, is Sherlock's confession. You're important to me. You don't want any more people to die, so I'm giving you your wish.
John thinks that maybe that's okay. At least he can tell the people where he's going that he was loved here. Because that's what love is, isn't it? He can see that that's a twisted assessment of the situation, but then that's probably why he and Sherlock get on so well. Twisted is perhaps the best word for both of them.
The shot rings out, and it's all John can do to flinch and wait. He waits a full two seconds for the inevitable (well, not-so-inevitable) explosion, and nothing happens. One second later he looks up to see Moriarty gone. There are still half a dozen little red dots on his chest, but he isn't being shot at. He thinks with a stab of amusement that they're probably £12 worth of laser pointers. Within the next one-and-a-half seconds, Sherlock is right beside him, making him promise that he's all right. And John thinks he probably is, for the moment.