For those not understanding that killing this dude would be bad, please read
@Meridis comment, it's pretty good and without spoilers... I think (I don't read the novel).
Those mocking (jokingly mostly) us "manga only" readers for thinking that she's trying to protect her colleague... the author added some bad dialogue here to make us believe that.
From what I understand from the comments, she just doesn't want Zeff being judged for killing a government official, but if that was really the case, she wouldn't spout shitty dialogue like:
"Could you leave it at that and put away your sword, Zeff? He's still technically my comrade, so I can't completely ignore this."
And blocking the MC's sword, and putting her body between him and that bad dude. Her actions are clearly agressive, and her words are worst.
There's no way to "misunderstand" what she means. "Leave it at that" is like her saying "just let him go free, forget and forgive what he's done, you punished him enough".
And her positioning and agressive stance clearly state "I won't hesitate to fight you to protect this guy".
If the mangaka wanted to leave us with a cliffhanger, with us not knowing what her intentions are, something like this would have been better:
"Please put away your sword, Zeff. He's still technically a part of law enforcement."
Then follow that in the next chapter with something like:
"I don't want his blood on your hands to make people doubt you."
Now I'm not curious about what will happen next (probably a short fight with him losing, then her staying her blade and correcting the "misunderstanding").
What I'm curious about is what kind of convoluted way will the author chose to make sense of this mess.