I'm trying to put this into perspective here. All of your love for the supplementary material does not change the fact that even in Robotech the show, Major Jonathan is a pretty one note character. It's like trying to get bent out of shape because someone killed off General Crix Madene in this one Star Wars book. Does anybody really remember Crix Madene from the original movies? No but the guys writing the Star Wars novels loved to use him so much precisely because there was so little to him, but hey he was still in the movie right? Hell Star Wars books are a great example of what happens when you let supplementary material try to fill in the gaps. It just gets ignored when the next big franchise push comes.
So yeah, its fanfiction. A wonderful manipulation of the setting and characters or just plain crap, but in the end none of it really matters.