I'm not sure anyone can quantify the horrors of war by stating that any one person is more or less affected. I think that they all suffered reasonably equally (okay, maybe some more than others, but I sure as hell can't say who), but for different reasons. Jake, "armchair quarterbacking his entire life" due to the burdens of his leadership, and all the people he got killed (don't forget him sending Doubleday's men and the auxiliary animorphs to their death, along with the more obvious example of Rachel). Rachel, obviously due to her death, and even more, due to her losing herself to the war. Cassie, for the fact that the entire war went against everything she believed in, and how her relationship with Jake kinda dissolved. Marco, in my mind anyhow, just made the best of the aftermath. He was damaged badly after the war, being (once again, purely opinion) basically Jake's tactical officer (his #1, as Picard would put it) and seeing how those decisions impacted the war, and his best friend. Ax ends up fighting a war he ends up hating, is disillusioned with his own people due to the decisions he has seen the result of, and, well, ends up dead as well. Tobias loses his last true link to humanity, the girl he loves, and for that matter, was trapped as a hawk.
So, yeah, in my mind, they all suffered equally, but in many different ways. Hard to compare different kinds of suffering, I guess.