I don't believe that stuff about being completely destroyed by war. In the least, not completely. Vastly affected, yes. But not completely.
However, I like what you said Think, about how twisted everything is. Jake liked the war. He liked Cassie. However, as much as bringing them together would be great, he liked Cassie more than he craved being together.
The reason so many people hate the ending is because it relates to real life. People read these things to escape and be fascinated, not to be reminded of what reality is like.
The ending is like the end of high school, where you knew nothing would EVER be the same. And no matter how many times you come back together and try to relive those memories you can't. You become trapped in an ever more glorious past. That's why its so sad about the Animorphs. Without the war, they were just inclined to stick to memories. And when the opportunity came to relive those memories (even though it wouldn't be the same), they wanted to.
As far as relationships that are created under tension I think I understand. I had a semi-relationship with someone who I was told not to have one with, and that was all our relationship was based on. Once the rules were gone, it was no fun anymore!