Killing children is one of the ultimate evils, and should be avoided at all costs. Hell, maybe if the Yeerks were looking for Karen, it could distract them, like Zone 91 and the like. I'm sorry, but Marco and the others didn't want to even try, and killing of that cold-blooded and ruthless nature should only be undertaken unless absolutely necessary. Like I said, Karen seemed like a reasonable girl, and after her time infested, I'm really sure she would've understood that she couldn't go out. The Chee have an underground park, food, toilet, bath, everything someone needs. And hell, if she got lonely, they could even take her to see her father under a hologram! She was shown to be smart, and like I said, reasonable, so I'm sure she wouldn't burst out. Cassie was the only one who understood this, in her own clumsy, moralistic way, but at least she got it! What if that had been YOUR children, hm?