I was trying to be as general as possible -- anything from sexual orientation to a bad boyfriend to sex'n'drugs'n'rock'n'roll to working as a drug courier to -- I don't know, becoming a Buddhist nun? I'm not suggesting any of those, but without knowing anything about the family and their personal, social, and professional values, it's hard to say what might constitute a lifestyle choice that they would find so objectionable it would require her to leave home in order to pursue it. It might be something that would seem ordinary to us. For instance, I know a younger guy who was the only musician in a family of scientists and mathematicians who was estranged from his family for years before they became reconciled to his choice of profession.
And again, I'm being hypothetical. The first time he said it, I thought he was hinting that there had been some sort of conflict of that sort but he didn't think it was bad enough she'd want to leave. But like you, on reflection, it sounds like he might have meant something else.
I don't know. There's just no evidence.