Silly question, I know. She wouldn’t have even been in his house; she was a Ravenclaw, after all. But they have a lot in common. They both played a direct part in the founding of Hogwarts, Slytherin as one of the founders, Helena as a founder’s child and part of the first generation of students. They both grew apart from the other three founders and eventually fled the castle, never to return. They both did something or took something with them that left Hogwarts in a fractured state. And they both played an unknowing role in Voldemort’s rise to power, Slytherin as his ancestor and inspiration, Helena by telling him where to find Ravenclaw’s lost diadem.
Helena didn’t have the greatest relationship with her mother, so perhaps there was another teacher she saw as a role model instead – and there’s not much Gryffindor or Hufflepuff about her. Perhaps she looked up to Slytherin and wanted to be more like him; perhaps he even told her that if she weren’t Rowena’s daughter, he would have picked her for his own house. The lover who comes to find her when she runs away was a Slytherin, so perhaps she associated herself with Slytherin house in other ways as well.
Depending on the timing, her decision to steal the diadem and flee might even have been influenced by Slytherin’s own departure. She didn’t steal it out of longing for the wisdom it could bring, but rather, because she thought it would help her become greater than her mother. That’s pure ambition right there. If she witnessed Slytherin’s fight with Gryffindor and subsequent departure, if she knew what he had left lurking inside the school, if she saw the growing fracture between the houses and perhaps felt torn between her mother and her mentor, she might not have had much reason to want to stay.