Sparing the main villain is just about my least favorite trope.
While Liberta is hardly great literature, I actually think it makes a lot of sense in this case because Liberta never really considered Elizabeth an enemy. She wants to stay neutral in Elizabeth's war against the humans, she isn't taking sides against her. She only fought her here in order to protect Komari. And well, they are still sisters after all.
And yeah, I agree with the other poster, I suspect this will end with Komari rescuing Eri anyway.