1. Cassie had a plotline (the YPM), but unlike the other characters' arcs, it was just glossed over and only used as a cheap "get out of jail free" card in #50 because we had to be reminded that it was still a thing that existed. That is an issue on KAA's part, but it's still a Cassie-centric problem.
2. The Departure? The only thing she sacrificed in that book was her own circle of friends. She basically handed them over to Aftran on a silver platter, when Aftran was literally right in the middle of a rant on how much humans sucked. Cassie had no reason to trust Aftran, and Aftran had no reason to not turn in Cassie. It was just pure luck that she got trapped in the woods with the one nice yeerk in the pool. That was no better than what happened in #50. And as for the ending, she was the only one who wasn't ambiguously killed off, so yeah.
3. I really hope you wouldn't be the kind to sell out your friends because the going got tough. Cowardice and foolishness are not an excuse for outright treason. If she were in any real army, her actions would be met with capital punishment. War demands loyalty, if nothing else. If you can't continue to stand by your fellow soldiers, the least you can do is not fork them over to the enemy.
4. Her development doesn't make any kind of sense from a reasonable standpoint. In#9, she's kind and compassionate... except to Tobias, whom she hurts by acting aloof, insensitive, and judgemental towards his personal crisis on the deepest, most personal level she possibly could right when he's opening up to her and offering to be best friends (and considering Tobias is my favorite character, that doesn't exactly endear her to me). There's a reason those two never had a conversation after #9. At the end of the book, she acts like she learned her lesson about it, but then in #19 she goes and does the exact same thing to Rachel in the name of "kindness and compassion," prompting her leave the group and sell them out to the Yeerks. Then, she does it
yet again in #50 towards Jake and hurts him even worse than anyone else by not only having a total lack of faith in him, but undermining and betraying him with physical violence when he has a shot at getting his brother back. After the war ended, instead of trying to help Jake get over his issues, she just poured salt into the wound by actively ignoring him and dumping him for someone else when he finally voiced what was plaguing his tortured conscience. See, there's a bit of a pattern here...
My issues with Cassie arise because her actions are in stark contrast to the kind, compassionate, understanding people-person she's painted as. She's got no impulse control whatsoever (which I think might be the reason she's the one who always loses control of her morph), and manipulates people into doing what she wants if she feels like she doesn't have enough control in a situation. She gets uncomfortable if she passes up an opportunity to keep the others under her thumb using moral double-standards as a vehicle. That's why she guilts everyone all the time. At face value, her actions make her a total monster.
That, or she's got bigger objectives in play. Check out this thread in its entirety.
http://animorphsforum.com/index.php?topic=10495.msg848341 I present a theory and we get way in depth on her character, covering all this and more.