I'm still up in the air about whether Jake should have been tried. Yes, everything he did was for the sake of saving the human race, and one of the dilemmas they struggled with throughout the series was the big picture vs. the little picture, and where to draw the line. And while I wish it weren't true, I was dissatisfied by the abrupt change in Applegate's style from the slow, character-developing stages of the series to the fast-paced, finish-it-now pace of the last several books, I can't say that this one detail was a sloppy one. It seems clear to me that giving Jake the exact same decision Elfangor had many years before was deliberate. If that's true, then the choice he made was also deliberate. I think this one is on Jake, not K.A.
But maybe that's the point. Elfangor made the choice that most people would think that they themselves would make in the situation. He was still young and naive, and had never really seen battle, never had to make life-and-death decisions. Jake was also young, but had been at war for 3 years. Maybe the point is simply that war does terrible things to people, changes them. The Jake from The Invasion wouldn't have made that choice, but 3 years of fighting and leading his friends into potentially deadly situations made him that much more ruthless.
And to your last point, I concede. While the Animorphs tended to show restraint when battling human-controllers (by the way, how many human-controllers had to go home and explain missing digits and gouged eyes every week?), they did seem to kill Hork-Bajir and Taxxons left and right. Definitely a moral compromise, but I guess there's a difference between kill-or-be-killed and kill-or-walk-away. If a 7-foot-tall bladed creature is swinging at me, I don't really care about the motive.