Was the commander there when Shiying was punished by thunder and fire?

Not here. According to the plot of jade bone Yao, the grand marshal was god of light, not a mortal, so the grand marshal was not present. The story of Shiying being punished by thunder and fire happened in episode 13. This is because Shiying was moved by ordinary people, and then punished by thunder and fire, and was banished to the world. The great commander is the god of light and cannot be present.