aftran is indoctrinated. i get the impression that she's...fairly young? certainly of the generation that has grown up in space, knowing only the empire. "we're no worse than the sapient predator species" is probably something you learn in yeerk kindergarten, on yeerk president's day where all the kids make banners of the emperor and visser three.
The other thing about Aftran is, we know from what she's said and done, she has doubts about the war already, before she met Cassie. That's why she took the job Controlling Karen, "so she wouldn't have to kill", and why she was so happy her brother had the job he did as backup security to a sharing meeting. She also at one point throws out as a side comment that the Yeerks have people like Cassie...people opposed to the war and who think it's wrong to take unwilling hosts. She never says how she feels about them, but the fact that she brings them up, and doesn't seem to do so in a bitter or angry sort of way is sort of a suggestion that maybe she isn't entirely unsympathetic to their ideas. She also points out contemptuously that the Vissers spend more time fighting each other than they do the enemies of the Yeerks.
They say sometimes that there's no stronger propagandist than someone with doubts themselves, because they're not just trying to convince you they're right, but also themselves. And I think that might be where Aftran is at the beginning of the book. She's not entirely convinced of the rightness of the Yeerk cause, but she needs to convince herself that it is right. It's easy to do when she thinks she's talking to an Andalite, because she hates them...they've been the enemy for like 30-40 years, but when she discovers Cassie is a human, she has to come face to face with the idea that the people the Yeerks are hurting aren't just the Andalites, but also humans, who are more or less defenseless and victims. So she gets defensive, and she gets really defensive when Cassie suggests that Karen doesn't hate Aftran, but pities Aftran. She can hate an enemy who hates her. It's harder to know how you should feel around somebody like Karen or Cassie, who pities you. She needs the hate of humans to justify what the Yeerk are doing to humans. When Cassie refuses to hate her, and is even willing to sacrifice herself for Karen, and for Aftran herself, it just completely disarms her.
And maybe it's just because Easter was this past Sunday, but I want to point out that Cassie sacrificed herself by hanging off a piece of wood, dying, and then resurrecting three days later to redeem Aftran from her sins, and if that isn't symbolism that hits you in the face with a two-by-four, well....