In making my speculation post I wanna say I'm of the mind to have a few assumptions here. I'm also assuming the intent was fully brought across in the english translation, but I won't cherry pick too terribly with exact verbiage - intent is what's important here, and inevitably some things framed in english will add nuance that was never intended to be there (hello possession v possession). Also I'm probably going to be in part or totally wrong here - but hey, that's the fun of speculation.
1. Motoori won't die.
This one's probably the most obvious. FS ending here would be rather abrupt, unsatisfying, and that being said...Yukari rather explicitly intervened mentioning she was aiming to 'save' Motoori. Which leads to assumption 2:
2. Yukari has an endgame here, and it isn't busting a youkai out of the scroll.
Or at least, not merely. If all she intended to do was do a jail-break for a friend, acquiescence, etc - she of all people would have an exceptionally trivial time simply nicking the scroll, and getting the seal on it busted. But pushing Motoori all the way over the edge did have a helpful effect here, which leads me to believe that:
3. Yukari's endgame is, primarily, cutting off the Youkai influences to Motoori and, by extension, the human village.
Right now, Motoori has: published Youma books for the kappa (unknowingly), distributed a newspaper for Aya (knowingly), and been approached by Mamizou who's rather borderline threatened her to gain access to her Youma books. As things stand, this makes Motoori a source of influence and power for two factions, and potentially a third. Of those, one of them even rather blatantly wants power and influence over the human village. Compounding this issue is that influence from the Youma books as well as actual Youkai is doubtlessly having an effect on Motoori.
As Yukari is rather keenly interested in the stability (not necessarily always the same as a balance of powers, but in this case it is) of Gensokyo as a whole, Motoori's status as '(un)witting pawn bringing about influence and power for various factions, especially over the human village' probably isn't sittin' well with her. On top of that - this is purely speculation on my part, but it doesn't seem like Yukari necessarily agrees with the fate FS has not so subtly foreshadowed's in store for Motoori if she keeps down this path of her own accord.
Key phrasing here being "of her own accord."
So far, the only on-screen transformation we know of from human to youkai was the fortune teller - but keep in mind that Reimu doesn't have qualms with Youkai as a whole existing, nor does it seem to be a sin for a human to have become a youkai (See: Keine). The key difference here was that the fortune teller deliberately turned himself into a Youkai and, as a result, intentionally violated that balance of power.
But wouldn't it be a different story if there was an out, an excuse - of someone becoming a Youkai not of their own accord nor intent? After-all, the night parade scroll is a dangerously powerful Youma book - perhaps the youkai inside's sheer presence is powerful enough to curse the reader. And if that's the case - hardly Motoori's fault, and if it isn't Motoori's fault, Reimu has no reason to put her to the sword.
Now, I don't necessarily think this is the only outcome. It's entirely possible that, if everything else I've said holds true, Motoori might learn to use the Youma books and control them whilst remaining a human. But the only outcome where a endgame of "promoting Motoori from a pawn so she can't get pushed around and forced to be a influence" makes sense is one where she has the power to fight back. And I think with all the foreshadowing in the past, it likely makes more sense for this to be Motoori's forceful push to the other side - and one that wasn't even her fault, since the youkai in the night parade scroll more or less forced her hand in a way that wasn't entirely (or perhaps even at all) of her own free will. But again, it's not necessary for her to become a youkai outright - simply learning to use the Youma books for her own defense would likely suffice to satisfy the demands of this theory.
Either way, I highly doubt this ends with everything going back to the status quo - it feels more like we're going down the path of a new meta-arc, one where Motoori has to deal with newfound powers. Perhaps if Yukari hadn't directly intervened I'd be more willing to buy that, but with her stepping in so directly I don't think this is going to end with Motoori "stop sticking your hand down the garbage disposal" Kosuzu remaining powerless. But her gaining powers doesn't necessarily mean that the status quo is irrecoverably changed - it simply means she now has the agency to make decisions beyond "agreeing with whatever decision people want to force down her throat," and can forge the truth she wants, for herself. With the convenient side effect of removing her as a easy scapegoat for Aya and co to push around as they please.
also this outcome allows for playable motoori in ACoF without her being the star of the show and man i love the parallels you can draw with motoori's appearance here and her appearance on the cover of volume 1