I would say all this falls into the "prisoner of fate" category and isn't necessarily a flaw or personal consequence of Sara's, but you're starting to see the more dangerous sides of her personality and if it's anything like the original those will result in very real failures of hers later. Sara needs saving just as much as Natalia does.
While it might seem noble of her to attempt to sacrifice herself to restore order, she's also willingly abandoning Natalia in the process. And there's no reason to think Luis is wrong about the sword yet (chronologically, since this is a flashback and ch2 hasn't happened. Yes the dire wolf does count as a monster).
It's a very hasty decision and Sara knows it's going to leave someone vulnerable, but she excuses it based on seeing Natalia's sense of duty when she was dying and delirious. Touching a bit on spoilers
if it's anything like the original Sara wanted to die before getting the sword, over what made her a nun in the first place. She's not being completely rational here.
Suicidal intent isn't inherently a flaw, it's a very sad thing, but Sara ignores the harm it could do believing it's the best solution for everyone.
You don't need a magnifying glass to spot the flags Luis was setting, but while he seemingly lied about pulling the sprout he is almost certainly telling the truth that the only way for Sylpheed to transfer is for the previous host to die. He doesn't want to sentence a good person to death just to heap more responsibility on his sister, who didn't want the position in the first place. Yes that means denying Sara's will in the matter, but choices with no clean solution are part of being a ruler.
There's an extremely relevant quote of his back in the first chapter,
There's a weight to choices made for yourself. A weight which only builds until the day you die.
It's one of the themes of the series, and when these two start making choices for themselves it's going to come down hard.
Another is good intent only making things worse.
