How could Glasya not run away?
The black dragon was so much stronger than what she had expect. She couldn't understand how one dragon could set such a different example of strength to his peers. While dragons have always been the strongest creature, it wasn't the first time for Glasya to take them down. She had even taken the lives of the previous dragon kings which make her well versed in how to defeat a dragon. While they have immense power, they are usually arrogant like Magnus which caused them to always make a single flaw in their fight which in turn becomes their weakness.
But Magnus had a rather twisted personality. He wasn't someone easily angered. Perhaps because she hadn't found out what could irk him, but now she had lost the fight as he was the one who had grasped to her weakness first.
It was even worse considering the fact that Magnus was taunting her using Rafael's face!