While I'm personally not opposed to the ideals the author tried to 'champion,' it was so poorly written that it did more to hurt the cause than help it, and KAA (her right, since it was her bookline) completely undermined it with the last chapter.
I think I know where the Author was going with Ax's line of thought about the animals, if you read the Andalite Chronicles, Elfangor himself was squeamish about the idea of eating meat and did call humans 'barbarians,' though that was more in reference to medical practices. It's not a huge stretch of the imagination to say that all Andalites would have the same views. But if you studied Ax's character and Andalite culture at large, it's just plain out of character for Ax to have those kind of thoughts (he was more of a 'when in Rome' kind of person). And Elfangor himself was mentally/morally on the fringe of Andalite society, at least for the military, there's no real way to claim that his opinions would be that of Andalite society.
While I think KAA definitely had the right to add her own ending, her statement kind of rubbed me the wrong way. I think she is definitely a morally conscious person, and she is masterful at writing her own cause in her series. But people saying things like "I'll care about W when XYZ happens," kind of strike me as a little closed minded. I think humans have enough braincells to care about more than two or three causes, even if they dedicate their time and efforts to another. People who work to put themselves out of a job deserve respect, no matter what they are doing as long as their means aren't nefarious. I'm not going to walk up to a person in a soup kitchen and go "I'll care about what you do once all the homeless puppies are saved" or say "Mother Teresa sucked at life because people are cutting down the rainforest!" I really don't think she meant it that way, but I think it's safe to say that KAA has demonstrated a lack of tact in some communications, which is really unfortunate given her amazing skill.
Overall, I liked the book, for obvious reasons (a large part of it being an Ax book, and when you're favorite character has half as many books you can't be too picky,) but I agree it didn't fit the standards of the series...and didn't even fit the series at all. If the author wanted to keep her job, she should have wrote a Cassie book. It kind of makes me wonder how the whole ghost writer 'job' works, if KAA put out what she wanted written on some secret website or if she sent out an ad or something, or just accepted manuscripts and said "okay it'll do lets print this."