The 9th circle, aka, the deepest and worst part of Hell, in Dante's inferno is dedicated to traitors (from the least severe to the worst):
- Treason against one's kin.
- Treason against one's home (as in city-state/kingdom/etc...).
- Treason against one's guest(s).
- Treason against one's benefactor(s).
I had a character, more precisely, a pair of characters who were spying on a king and his court. One of them was a robot, called Maria, with the ability to assume the form of any human; the other one was a female lizardfolk, supervising the operation.
The example story (will be referred to later in the question)
While it was careful and passive surveillance for the most part, after an unsuccessful attempt to replace the king, they're forced to run. This is where M. comes in.
M. is a typical amnesiac protagonist, who takes pity on the two and aids their escape. During this, they have an opportunity to get to know each other better. The lizardfolk was told that humans hated her kind, plus she grew up in a bunker-turned-city, which was a constant reminder of that. It comes as a surprise to her that M. doesn't treat her or Maria any differently than his comrades.
Anyway, after realizing that M.'s seemingly useless ability, The Hermit, can be used to interact with ancient technology, she forges a plan and takes him to another ancient bunker city under the pretense that maybe they find clues about his lost memories there. So, they go around the place, activating ancient technology with The Hermit.
Eventually, M. finds out the place was designed to be used as a weapon, and his actions brought it to an almost-usable state. Maria and the lizardfolk realize that and knock him out. The two place him into an elevator, going straight to the surface. They delay the last steps until he's out of the maximum-security zone.
Now, when they bring the weapon online, they don't intend to use it, it's a bargaining chip. They don't know that the weapon was set to fire on the closest human target (a peaceful city, in this case) the moment it is brought online, nor that the lizardfolk's root access to the system is actually a false root that doesn't have the privilege to overwrite the weapon's orders.
I'll stop here for now.
Obviously, this lizardfolk is supposed to be a less-heroic but still good person, whose actions could believably cause someone (the king) to try and murder her even though she's unarmed and reluctant to fight. I'd say I did a fairly good job with that. The problem, as you guessed, is what she's doing to M.
M. risks a lot to help her, has no prejudice towards her kind, and happily assists her with what she asks. Even when he finds out the truth, he wants to talk her down.
So, using that person's trauma/disadvantage to trick him into doing your bidding is not nice and according to Dante Alighieri, is literally the worst sin a mortal can commit.
That's good for a villain, bad for a sympathetic character.
So, how can you keep a character sympathetic after they committed the treason of the highest order (i.e: they betrayed the one(s) who cared for them)?