That's right! Or rather, he has the ability to do that, but not easily, and he is not willing to pay that cost again right now, let alone for one person, no matter who it is. Resurrection is not an on-off switch.
To start, even someone like Harrow at the peak of her worship when she thinks the 500 newly-Ninth are freshly risen words it as "You've committed Resurrection", like committing a crime or a horrifying act. John corrects her there and clarifies these among others have been Resurrected but in stasis (a necromantic version of cryostasis!) since The Resurrection. There has only ever been the one.
This is referred to elsewhere but especially spelled out by Harrow-with-Alecto's-memories in the dream; we don't have to rely on John's word, Alecto knows so Harrow knows. Resurrection is different from waking up. He Resurrected a lot, but first woke only a few thousand, then some hundred thousand, then millions, but never more than millions, and all those he's never woken have been in reserve ever since.
When in that first instance Harrow asked why he hadn't done it since, he says the cost is too great. Later, when he learns the full details about her parents and her birth, he says they committed "a type of Resurrection." So let's examine that. If the Reverend Parents were willing to murder an entire generation to keep their bloodline going, wouldn't it make more sense to leave just a few kids alive, perhaps 2-3 of each sex, barely a difference from the total but just so Harrow would have a few options / spares if some of those didn't make it to adulthood to produce further heirs down the line? The only way it makes sense to sacrifice every last kid except the one required for the House to function is if they weren't sure 200 would be enough.
And that's further supported by Teacher, the priests, and the Hideous Corpses! As indicated by the pinboard, it takes 3 or 4 souls to power the simplest of those just-fancier-skeletons. (I say "or" because we don't know if the white pin represents the skeleton with its original soul or just the physical skeleton. The smallest clusters have 3 colored pins around one white pin.) Some of the skeletons take more than that, and it takes hundreds to power Teacher and the other two priests, with the 500 total souls between them and 47 skeletons effectively acting as a hivemind.
Magnus has also told us that the common belief in the Nine Houses is that souls wait in the River "for our Lord's touch on the day of the second Resurrection" (which itself lines up with a lot more references John makes to wanting to Start Over). He plans to do it again, in a way, eventually, but he won't do it until then.
We don't know all the details, but all evidence suggests it takes many souls to Resurrect one, and that he never could have brought back all ten billion even if he'd wanted to. There could also be additional layers we don't know yet, but whatever the case, it's not as simple as him choosing not to flip a switch just because.
Bonus theory! Language seems to have power in some way in this world. Steles need to be covered in dead languages and those carvings need to be kept clear of build-up and bathed constantly in fresh blood. (TL;DR my theory on those is they appeal to the ghosts of the ten billion and use their power to warp time around ships rather than technically making them move fast but not the point here.) So with that in mind, it's interesting that every single instance of Resurrection and even Gideon's pseudo-Resurrection comes with a name change. There isn't a single exception.
And more than that, the first time John ever makes Ulysses and Titania move, even if still dead, is when he introduces them by their new names for the first time. And I mean, a point is made about how much John hates change, and Tamsyn Muir has mentioned before in interviews how he falls back on systems because they're familiar, even when he's actively struggling not to. He doesn't seem like the kind of guy to make himself relearn everyone's name just for fun, does he?
So I think it's entirely plausible that Resurrection in this world inherently involves a sort of reinvention. Mercy used to be M— but Mercy was never quite M—, etc, in the same way Paul used to be Camilla and Palamedes but isn't either anymore. The old you is dead, and nothing will ever change that, but you-slightly-to-the-left—a legally distinct you, if you will—that person can still have another round at life.
(Which if true could suggest some surprisingly hopeful things about John giving Gideon her own name back, just transcribed as it would be in Te Reo Māori. But yeah!)
All that said. No idea if he could have done the same thing to a living body or not; it'd have really interesting implications for the limitations of his powers if he couldn't. But if he couldn't or even just not as well, I mean, making her body indestructible BOTH so no one could take her blood AND so no one could take her away from him after he'd just lost damn near everyone and everything else all at once may not have been the primary goal, but I'm sure it was on the list of pros for him for sure. 😭
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