The Animorphs series was never a bunnies-and-rainbows-everything-works-out type of story. And I think that she defended her writing wonderfully in her letter to the fans that didn't like it. The gist: one war usually leads to another. Tom was right, wars are never fought with clean hands. And people die.
For all of them to get through the whole thing unscathed and come out perfectly well-adjusted human beings was just unrealistic. How many war vets do you know that are at least partially shattered by what they have gone through? How many do you know that moved past it with absolutely no baggage?
Jake was a child when the war began, he was an adult when it ended. And yet, he had spent so much of what I will call his adult life--his life as a commander--pretending to be the average kid that he didn't know how to deal with peace. It wasn't like Rachel, to whom the war was like a drug, because he didn't want it. But he didn't know how to live without it.
So, yes, I thought the ending was appropriate, fitting, thought-provoking, and bittersweet. Not happy, of course, but it was a war story after all. If you expected it to end happily than you should research the wars that have been fought through our own history. Name one that ended happily.