That's obviously is one of the worst thing she can do... Killing someone in front of the ML. But tbh it was justified since she was panicking and have been through a lot. Also, she doesn't have a choice. It either getting rid of him, or repeating the cycle once again....
This guy is a jerk. He needs her because shes useful and sees her as a tool, not because he loves her. Theres no way to justified the fact that hes very neglectful to her. Hes just a plain scumbag. I Hope in the second timeline he will suffer , the empress is better without him, i hopes she...