Not an AoT manga reader, so my take:
According to Reiss's narrative of events, the OG Royal Titan created this whole scenario as a way to "save" or preserve humanity from extinction. No one ever gets a straight answer from the Titan Kings after they "ascend;" the status quo is preserved, even though any of the lineage could have freed humanity and ended the 100 year nightmare.
If Historia went spine sucking here, she'd effectively become an amalgam of her royal lineage; an unrecognizable, different person. As herself, she's seen all the suffering and insanity that humanity endures in their fragile walled city-state. She also knows that, based on all the other generations of this, Ascended Historia would sit back and do nothing too, regardless of her present convictions, because of whatever knowledge or memories that would reshape her perspective like it had for all her predecessors.
Reiss presents this all as the righteous and necessary path to save the world. But, based on what we know, an Ascended Historia wouldn't save the world. She'll learn the Truth, that will transform her worldview, she'll get the walls back up, brainwash everyone and act to preserve the old status quo. She also knows that the organization of titan-humans outside the walls have some unknown motivation to disrupt the status quo at any cost. While their measures are extreme, and the cost of life enormous, it's nothing compared to what the government did in response to the initial attack. Far more people died in an intentionally designed suicide re-taking of the lost ground, while the nobility filled their bellies and the refugees were starving and sent out mostly to get eaten.
The outside rogue actors are breaching walls and trying to take Eren -- as the vessel for the Monarchy's omnipotence and subjugation of humanity -- away from the reach of the Reiss's. We know they're hardcore and mass murderers but they've deemed their actions justified based on the undisclosed knowledge they possess about this whole scenario as well. And we know they're not true monsters based on the years of comradery the Scouts had with them. Ymir's bond with Historia and all of her actions in the previous arc, combined with what we now know about the true monarchy and its role in reshaping the world introduces a lot of ambiguity about which side is fighting on behalf of humanity and a free world, right? Levi brought it up, too.
Historia doesn't want to become another vessel for the original architect of this whole insane situation. She doesn't want to lose herself and become the person who would fulfill the architect's role yet again. Incomplete information and unreliable narrators abound, but Historia stops and looks at what she's about to do. She's about to commit to eating Eren and her goals will probably evaporate with those cold new eyes. She's about to rationalize it to herself as her duty on behalf of humanity, but none of these prospects actually align with her values as Historia the human being, and humanity is starting to look like one giant clusterfuck with her family at the center of it.
What seals it for her is Kenny's wild card of unlocking Eren's Titan powers. Reiss encourages her to go all out and slurp dat spine, do or die. But Eren's not transforming. Eren is crying, overwhelmed with grief and self-loathing, and asking to be eaten as a way to atone for his father's (...ambiguous) actions and all the blood spilled on his behalf and as a result of his unwanted powers. He's presented as humanity's enemy by Reiss, a necessary sacrifice to save the world from destruction, but he's the one overflowing with humanity in that moment, internalizing all the suffering, fallen friends' names vivid in his mind, and firmly willing to sacrifice himself in gruesome final death, contrasted with Historia's prospective level up to godhood and the sole recipient of the Truth.
She shares many of Eren's virtues on the surface, and yet he's pushed himself to extreme lengths for the sake of his comrades, his fellow people, and he wants the titans destroyed and humanity freed and she knows that for certain. Eren wears his values and his convictions on his sleeve, and she's staring right at the manifestation of that in the deciding moment,
Historia realizes that the syringe pressed to her arm represents her induction into Team Evil, and it's time to burn it all to the fuckin' ground, not perpetuate the cycle of subjugation and horror. Eren, as an alternate vessel for the Power is a known quantity. Kill the monsters. Protect his friends, no royal dark side powers. Ymir operating on Team Beast and yet firmly remaining someone she believes to be a good person further complicates matters. They want Eren's power out of the grasp of the monarchy and in their control, and they're directly responsible for atrocity and massacre of civilians, but their endgame is unclear.
Too little hard data to work with there for her, so she stuck with what she truly knew about the people involved instead of anyone's narrative.
Deftly executed and defining character moment for Historia.