Incoming wall of text
[spoiler]I have to say having given this subject quite a bit of thought, I was deeply disappointed with the ending. I can fully sympathise that to draw the series to a satisfying conclusion is a very tricky task. Unlike some, I don't view KA as a bad writer in light of this; I think she should be commended for creating such an enjoyable universe with characters that the reader can empathise with. I do however think KA stumbled at the final hurdle, and that the ending seems rushed and not particularly logical.
Whilst it is indeed KA's universe and she can write how she sees fit, readers are not forced to accept an author's vision of a universe. At any time readers can refuse to accept the terms and reject something as part of the canon. However a well-written universe persuades the reader to accept this view. If KA kills a character, I don't accept it because she - the author - tells me to. I accept it because through the narrative she has constructed, she convinces me it is the logical thing to happen in the universe, and ultimately this universe is one I find entertaining.
To that end, I personally reject The Beginning as part of the series canon, and I will explain why. I do however respect KA's own vision, and those that agree with her vision, but it is not one I share based on the universe she has established over the course of the series.
My rejection of the canonicity is certainly not merely because KA kills Rachel; characters have died in many of the works I have come to enjoy over the years and I have accepted them, even if I find them sad, simply because they follow the continuity and established logic of the universe. For example, Dumbledore's death in HP follows on logically. I might not like it, but I readily accept it as part of the canon of the HP universe because it follows. It makes perfect sense.
This doesn't follow with Rachel's death, because it was entirely avoidable by half-decent planning. Something Jake managed to show for 52 books, during which he took part in countless battles. Whilst it would be entirely unrealistic if Animorphs was real, this was part of the suspension of disbelief. Like the morphing technology, readers accept the - at times improbable - repeated survival of the major characters whilst many others die around them because the series has always been focused on these characters, their goals, motivations, actions, and thoughts.
The reader has to implicitly accept this as part of reading the series; if they didn't, they'd simply stop reading. This is part of the terms of the suspension of disbelief. Killing such a character at the final hurdle violates the terms of this, unless the author is able to convincingly justify the decision. This is before we even consider the manner in which this occurred.
The main themes behind the characters are at the core of the Animorphs series, and used to explore the human condition. Winning the war was secondary to the reader; it was this exploration and interaction of the characters that was at the heart of the books; the war was simply a backdrop to do this. Killing off a character because "war is nasty" does not follow from these themes; it is a non sequitur.
KA also attacks strawmen in her justification on the ending, arguing that readers wanted a perfect fairy-tale ending. Whilst some undoubtedly did want this, I feel it is fair to say that the vast majority were not asking for such an ending, and it would have been deeply unsatisfying. I personally would have had Tom killed off for that bittersweet ending. I would have had Jake break down after the immense psychological trauma, now the situation is finally over. I would have had him struggle to reconcile with Cassie afterwards in response.
I would juxtapose this against Rachel and Tobias's relationship by having Tobias successfully help Rachel come to terms with the end of the war, and the changes that had occurred to her during it. It wouldn't have been a fairy-tale ending where everyone walks off smiling in to the sunset. It would show the cost the war had on the characters, and it would give a chance to explore the recovery. In a series filled with destruction, blood, sweat, and tears, there is absolutely no need to destroy one of the few positive things merely for the sake of pointing out that war is horrible and has costs. There certainly isn't a need to do so when by doing this you then destroy the motifs behind an entire series of books.
One should also consider that there are survivors of wars. There are men and women who have suffered immensely, but they do recover. It takes strength of character, and support, but these brave men and women succeed. The Animorphs ending conversely does not show this, at odds with the strength characters have displayed for 53 books. Would this not be a far better and consistent theme to end on?
The state of the characters after the war is not encouraging. The one person who gains the most and suffered the least goes on to live a dull existence. Everyone else loses something. There is no struggle to rebuild. No themes of love and friendship allowing terrible situations to be overcome, which is at the very core of the books. It's simply a tale of needless destruction and misery, and the sole justification is a point that could be readily achieved in other ways, already features in any case, and because KA wanted to get across a very bleak message. It is the very antithesis of the core themes in the Animophs series.
KA's other justification for Rachel's death is that Tobius must remain sad. He's always been unhappy and this must remain the status quo. What kind of message is this to send? That those that suffer immense hardship should just give up because they will never be happy and it is pointless to try? This is not only repulsive, but again, the antithesis of the themes of love, friendship, and hope that drive the series.
And what of the other Animorphs? One can presume that James acts as KA's mouthpiece when he rightly declares that their lives have value too despite their disabilities, yet KA kills them off by sending them off on a suicidal death charge, with barely anyone noticing. Ironically KA only succeeds in getting the message across that such people are disposable and unimportant here, at odds with the message earlier on in the series.
There's also the finale itself. This comes almost out of nowhere and is essentially deus ex machina, a second fight to end on as a cliff-hanger, and a very cheap and unsatisfying reason to bring characters back together after destroying their relationships. This is deeply unsatisfying as a plot device, and feels very rushed.
This issue is very polarising. Whatever view you personally hold, I respect your right to feel that way, and at the end of the day, I feel this is an issue that everyone has to decide for themselves. Hopefully this has been useful for those of the opposite view to understand the rationale behind those of us that disagree with the ending.[/spoiler]