Actually, I think it's even more complicated than that. Remember Elfangor's last words to Tobias?
[spoiler=The Andalite Chronicles]
The Yeerks came and I told the human children to hide. But Tobias stayed behind with me for just a few moments. Alone.
<Your mother ... tell me about your mother, Tobias. Your family.>
He was surprised. Troubled. "She . . . disappeared. When I was just little. I don't know what happened. I guess she died. People say she just left because she was messed up. They said she never got over my father. I don't know. But I know she has to be dead because she'd never have just left me. No matter what. But maybe that's just what I told myself. I don't exactly have a family."
It was a fresh stab of pain in my hearts. And yet, I knew now that all was not lost.
<Go to your friends, Tobias. They are your family now.>[/spoiler]
That little dialogue hit him really hard when Elfangor died. A random stranger who seemed to care for him, suddenly brutally murdered as he watched helplessly. It made him want to cling to what he had all the more, and he risked his life over and over to keep his friends alive and together. In the finale, when Jake lost his family, he kind of started to push everyone apart with his distrustful, isolationist, "gotta put on a strong face for them" attitude. Tobias picked up on that, and really didn't like it. When he saw Jake actively excluding Cassie from the meeting, when she'd always been part of the group since day one, he felt like he had to step in and take a stance or else this surrogate family of his would fall apart, and he'd be alone again. That thought just scared him too much, so he called Jake out on it.
He had to have felt betrayed, but he couldn't just let go of the bond he'd built with the others. Even though Cassie wasn't exactly close with him, she was still part of the group, part of his family, and family sticks together through everything. In my Tobias thread I mentioned he spent a lot of time coming up with an idealized view of how things should work because he had so much going wrong for him. This is one lingering echo of that.
This is also why he just couldn't stay around after the war ended. It wasn't just that Rachel sacrificed herself. If that were all, he would've been able to handle it a lot better. But the issue was that Jake, the guy he originally pushed to be the big protector of the group, ended up becoming the one who sacrificed it. It mirrored the whole ambiguous duality theme that traumatized him so much with his torture. Regardless of whether Jake's actions were justified or not, it felt like a betrayal on a level he just couldn't handle. Jake was suddenly worse than Tobias' aunt and uncle combined while the whole world celebrated his heroism.
