>>15469946We don't know a whole lot about Atem's personality in ancient Egypt. He was definitely more wise and merciful than most, but we could be grading on a curve. Plus Atem did lose all his memories when his soul was bound to the Millennium Puzzle. And after Yugi finally assembled the damn thing, Atem was typically only being summoned in self-defense situations against legitimate murderers, psychos, terrorists, etc. So the harsh punishments wouldn't be terribly out of place, landing him in the tweener role more than an outright heel.
The turn back to babyface was largely due to Yugi's influence. They both made each other better. Atem became more compassionate and Yugi became more confident.