The main path choice changes the dynamic. Please, no spoilers... But it gives purpose to the issue you have a problem with.I don't know why but looking back on it the mc family should be safe. no smart organization would corrupt a employees family they would be off limits. 1 to instill loyalty 2 as a threat to betrayal. If you look at mob stuff you don't f with family even the goverment uses this for the army. A organization like this would not survive if it went around tortured and enslaved employees family and loved ones 9 out 10 times it will be a cycle of having to deal with constant employees fighting back then dealing with said person and hiring a new one over and over again. That would not only cost money but a annoyance to the organization and a minor threat of exposure. Are the few girls in a employees immediate family that needed or worth it when they have a whole town. There are plenty of fish in the sea. I don't know if it is just me but it was just bugging me.
In normal circumstances, yes... I completely agree that blackmailing or harassing an employee's family members like that would be a negative, immoral, contradictory thing to do...
But in the protagonist's situation, things are dynamically different. When the mask comes off, it is supposed to explain everything without literally spelling it out for us.