I don't think he should have stayed with them for reasons stated above, but I do agree that Sisko probably did make his decision in part because he was a father too. He knew how unhealthy that boy's upbringing had been and also how damaging it was to him. Just because his people did something very horrible didn't mean that he needed to suffer psychological abuse under the guise of loving intentions.
Of course, a part of me worried about what sort of upbringing he'd have on Cardassia.
Stay with loving but dysfunctional family or learn to be a Space Fascist.