@Lord Raziere:

I don't know the first thing about alchemicals, but I am a good at creating stuff, particularly characters.

So, there are a couple of ways to make your character's noble instincts less typical.

1.) She's compensating for an opposite earlier behavior. Basically, strongly corrupt or degrading origins of some kind. Not sure how this works in your setting, but things like enslaved, prostitute, street orphan, part of corrupt family, or the like. She may have originally been complicit, part of the badness until it stained her deep inside. Or she always hated it and couldn't wait to escape. Now that she has, she is seeking to prove that she isn't tied to that old life, that she can escape the darkness that she remembers from back then.

2.) Amnesia. Yes, this is basically the cliche-in-a-bottle, but that doesn't always make it unusable. Instead of the full-blown thing where she wakes up some day not remembering anything, I'd go for something more like there was some terrible secret that she learned that was very dangerous. To conceal this truth from the world (or maybe from herself), she intentionally deleted portions of her past or constructed false memories of some kind. This manifests at times as a semi-delusional nature, as she acts on or refers to things that seem to others impossible (because they never happened and are part of her false internal narrative of her past).

3.) Tragedy. You already have a heaping dose of it in part two. But, as in many things, the stuff that hits hardest is underlined and bolded when it comes in a familiar package. I suggest that, not only is there a motif of self-sacrifice, but that it hearken back to some original mistake or choice that your character made, perhaps early on in life (again, I don't know anything about alchemicals here, sorry). Every time she treads similar ground, even across incarnations, she relives the event. Stuff would be like loss of a child, responsible or proximal death of a childhood friend, killed one of her parents in an accident or misunderstanding, stuff like that. Now, later in life, when she makes these choices, she relives the earlier trauma and is wracked with self-doubt; is she really being noble, or is she just doomed to act out the same mistake over and over, like some farce of her own life.

4.) Institutional complications. You mentioned infiltration. Well, we all know from many a spy thriller or story of espionage, that there are many and varied issues with long-term exposure to false identities, collaborating with the enemy, and so forth. Add in some drama involving her infiltrations. Maybe she had a partner, or her mentor. Super great guy/gal. Taught her everything. But, in the end, this mentor was his/her own worst enemy, and was so good at pretending to be someone else that their original self vanished over time. Money, corruption, despair, the mentor gets involved in it, and eventually almost drags your character down as well, embroiling her in some dark scheme. Eventually they had a parting of the ways, but she is still haunted by her mentor's fall from grace.

5.) Reversal of fortunes. Maybe your character once had the Midas Touch, and could do no wrong. This new shift to constantly being her own worst enemy, but for the good of all, may be a new thing. Child prodigy is an archetypal example here. Someone peaks early, and then finds the rest of life difficult to cope with, as successive failures mount and the glittering memories of youth turn to dust. This can be even more painful for long-lived beings or reincarnations, as the cycle can repeat and the impact compound over time.

6.) More virtue than brains. Pretty self-explanatory. Maybe your character is just really bad at thinking about herself, and so reflexively crucifies herself without understanding the implications for her sense of self. This can go anywhere from gentle idiot-savant to self-deluded crusader that believes that she can endure anything on behalf of her cause. The real victim is your character's self-concept, though, as a grand, shining goal is good, but it is rather cold and remote, and maybe smacks of doing what she thinks is right not because it's what she has decided, but because of external influences or a concern for how others would view her. In the end, if you don't like yourself as a person, you aren't going to be a very good crusader (or you will simply be a very short-lived one, as burnout is a problem for those that can't shoulder the burden for the long haul).

Alright, well that's a start. Sorry about conflating 2nd and 3rd person there. All just suggestions, too; if you don't like them, we can try and pin down exactly where you are looking to take this.