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Sherlock knows John.
Not in that vain way that a man knows an acquaintance, nor a parent their child, nor a spouse their lover—no, Sherlock knows John deeply and intimately, as if he'd peeled the man's flesh from his bone and studied his soul with immense intensity. Sometimes, in the past, Sherlock would look at his flatmate and be able to deduce exactly what he was thinking and every step of how he'd gotten there. Once, he'd extrapolated backward so far that he'd had to stop due to the sheer wealth of information that was presented to him.
Sherlock Holmes could write a doctoral thesis on John Watson and could speak on and on for eternity, explaining every quirk of personality, every flaw of skin.
So yes, of course Sherlock knows that John will be furious once he realizes that Sherlock was alive the entire time. He may not anticipate the violence that will occur at the reunion (largely because he simply does not allow himself to think about it), but that is not a signal of a frayed understanding by any means. So, when Sherlock has his messages to Mycroft open, he finds himself wondering what plan to follow—
He will have to fake his death, and he will have to go to the Continent to hunt down and destroy the rest of Moriarty's network…but should he bring John with him?
The question eats at him, burrowing deep into his bones and just sitting there, aching. It would be profoundly dangerous for him, yes, and Sherlock certainly does not want John to be in danger…but the man thrives in it. It would be hardcore and fast-paced, but John was part of the military and still craves those adrenaline rushes, so that won't be an issue. Yes, Sherlock is even sure that John is willing to cut off all ties with his friends in London in order to come with Sherlock—he's too loyal, too determined. John would be perfect for this kind of mission, and he'd see it through to the end gladly, even if they both get captured and tortured and die in agony.
John Watson on the run would be ethereal.
But still, Sherlock types LAZARUS into the message box and hits send and then goes hurtling toeard the pavement below.
The issue is not that John is unequipped to handle the mission, the issue is that…well, Sherlock is selfish.
John will do fine on the mission, but he wouldn't enjoy it—he'd like the thrill of the hunt and watch in wonder at the mind games that Sherlock would surely play with Moriarty's chess pieces, but the majority of the mission won't be like that; instead, it will be slow, dull, boring. Sherlock will spend weeks in little towns in the middle of nowhere, proverbially hiding in a trench, trying to gain ground. He will be researching at every little town hall he can find and integrating into communities in order to find moles. Sherlock will spend so much of his time away in a stationary position.
As for John Watson, well…
John is a hypocrite.
He claims to like the peace and quiet, loudly bemoans every one of Sherlock's eccentricities as he tends to those that Sherlock has offended, and thus the entire world (including John himself) have come to the conclusion that John simply suffers through Sherlock's presence out of fondness…but that's not it at all. No, John adores the work, the violence, the sheer unpredictability of Sherlock's daily life—he craves it like an addict.
And when they're between cases, Sherlock goes insane, yes, and he's desperate to keep working—but so is John, as much as he loves to hide it, and Sherlock knows (feels it, deep into his aching bones) that John has not remained at 221B Baker Street because he's fond of Sherlock, but because he knows he cannot find the same high anywhere else.
They're both fucking addicts.
And so, Sherlock cannot take John on his mission because their companionship simply will not survive it. John would not be able to handle the lulls in between action because he cannot draw the same satisfaction from the private, intellectual games that Sherlock does.
He would do his duties, and he would do them well, but he would always resent Sherlock for allowing him to come.
And so Sherlock falls from the roof, grim and determined—
He will survive, and when he comes back, John will not associate him with the dull monotony of mainland Europe; he will only ever know Sherlock, bright and vibrant, in the heart of London, the greatest city in the world.