I've always figured that they should just add an account unlock for two possible same gender-romance characters, one male and one female. Available when you get your ship. Then they don't have to redo the existing dialogue for the other companions. They could even come up with a story about them being a stowaway that you just find there.
I know why you have that idea and while it could be done quite well, I think it would too easily lend itself to an abusive power dynamic. I'm not saying it shouldn't be ruled out, but the story start itself seems, to me, to be a bit problematic.
Also, how would those post-50 get the companion? For some classes this doesn't make sense - my Phantom would have far better security than that, but the Mantis (BH ship?) seems like a leaky rust-bucket.