Complex sentence: However, she will not kill Kōta and Yuka though this is only because killing Yuka this would upset Kōta, though that doesn't mean she will refrain from seriously harming Yuka.
Split into simpler sentences: However, she will not kill Kōta and Yuka, though this is only because killing Yuka would upset Kōta. That doesn't mean she will refrain from seriously harming Yuka.