I think it's a whole thing about how minju's family sees hayoon. From hayoons POV she's just a "play thing" minju begged her dad to bring home, hayoon knows how big minjus family business is and that the father doesn't approve of the relationship. She gets confused with minjus actions, doesn't know if she's genuinely in love with her or just obsessed with her "play thing". She feels that soon, when it's time for minju to take over the company, her father will force hagoon out and have someone else come in to be a more "suitable" mate for the family image, or worse, minju will leave her for such reasons after taking over the company.
Hayoon is an orphaned ressessive omega who was brought into a powerful rich family, she feels no matter how much she likes/loves minju that she'll eventually be thrown out, so she's swallowing her feelings and trying to get out before she has to suffer the heartbreak further down the road.
I feel bad for ChaMinju, and I still don't understand quite well why Hayoon is trying to cut her out of her life. (￣∇￣")