Yeah, I agree with several recent posters here. There's no reason Applegate should have made an ending to please her fans with. It was her decision to take the story where she did. What, should Shakespeare have made Romeo and Juliet survive in the end? He could have, but he didn't.
The entire Animorphs series was pretty dark. Even the dumb filler books had their dangerous moments--remember the Helmacrons shrinking the characters down to their size? It's a series about humans, not immortals. Some of them will probably die, some of them will get their feelings hurt. I'm a lot more satisfied with the ending than I would have been with "Jack and Cassie got married and Ax was their butler and everyone lived happily ever after."
Think about how the ending made you feel. Angry, confused, sad? The point is, it made you feel an emotion. It's saying something that Applegate was able to make her readers care enough about the characters that they reacted to the ending this way. The idea that she should have made it end happily because we were paying for the books is just stupid. We pay to go see movies too. In some of them we get attached to characters as well, and they don't always have happy endings. We weren't paying to tell Applegate what to write for us--we were paying to hear what she had to say.
Now, I'm not saying you had to like the ending. There are some valid criticisms of it: I for one would have preferred a villain we were used to appearing instead of The One, for instance. But it was still Applegate's ending to write, not ours.
And honestly, I'm amazed that she had the Animorphs defeating the Yeerks at all. How realistic was that, seriously? I'd say she threw the fans a major bone.