We are in no position to know God's thoughts. On the other hand, I think we need to give Him thanks for protecting us from the bigger evil that was planned for us.
God allowed WWII to happen, but he saw to it that we won. The weather clearing at the last minute making D-Day possible, the fog lifted in the Ardennes allowing air support for our guys at the most critical time in the attack. Development of the A-Bomb just in time to save us from having to invade Japan. All of this was God's protection, IMHO.
While I believe that God uses evil people to punish nations, I firmly believe that any discussion of what God allowed to happen, needs to also look at what He kept from happening. Personally, I thank Him every day for stopping the bulk of the 9-11 attack.
God was also supporting the Germans and Japanese from their point of view?
But they lost. How confusing.