1- same shit happened in anime, they are hated by both sides.
2- they are angry at him for refusing to kill unless he need to because those who survived might kill their friends. Kira ignored them. (Kira alignment is chaotic good, that why he have a lot better relationship with characters from male MC route because they not from army)
3- again, joining main guy doesn't mean he is better in game.
In anime, Shin agree with Zaft goal, he doesn't agree with it in game.
4-They are in army, they need to follow orders.
P.S: can't wait for SRW crew to meet Age 3 main character. After all, Kira don't try to force other to follow his no kill policy like them ( Age 3 main character like to do that shit)