And even if they did, that's just the author saying "Actually look at all these noble and honest people who were tricked in to doing things they regret, but actually they're going to make it all right and then nobly let themselves be executed because actually our society is so noble and good and the bad thing that happened was a deviation from the norm".

Like basically the thesis of FMA:B is that that everything Japan did in the 20s and 30s was bad, but the officers who did all the war crimes realized that what they were doing was bad so they overthrew Hitler/Hirohito and instituted liberal reforms and therefore they have totally redeemed themselves. The role of the US in razing Japan to the ground, and the Soviet Union of kicking Germany's teeth in, is completely removed from the Narrative so Japan can redeem itself without the humiliation of losing the war.