Lilly was in a bad mood, really bad mood but she was controlling herself. Anger was one of her biggest flaw and she wanted to control it... atleast try to.
That's why she made she was in a good mood before coming here but the sight of Obligator supporting someone so closely infuriated her.
He was breaking rules set by her father, which was basically like slapping his face. Lilly knew she was overreacting but she didn't care.
Arthur Pendragon held a special place in her heart and she would kill anyone disrespecting him. However, here she controlled her anger.
Simply because of two reasons. First was obviously to gain a perfect control over her raging emotions. And second because of William.
She didn't want to interfere in his life or more like she didn't want to hinder his growth. This whole fiasco with Verley Clan held a special place in William's life and he needed to resolve it himself. Otherwise, he would have heart demons.