IF the Doctor had never told Seska that the baby was not Chakotay's then Cullah would have left that baby on Voyager alongside the body of his dead mother. All it took was for the Doctor to have decided to keep that information to himself for strategic reasons or for Seska to have not brought the baby in for a check up in the midst of her hostile boarding and acquisition of Voyager.
Such a small set of events.. without them they would have found the infant in Janeway's ready room. Would they have kept him because he was half Cardassian and so from their quadrant? Or would they have returned him to Cullah if possible?
Since Cullah agreed to have his lover impregnate herself with another man's child for the sake of luring Voyager into a trap I suspect Janeway would have declared him a hostile and unfit father and taken the baby with her. Naomi would have had someone to grow up with. Hopefully the Cardassian smarts would have been dominant.
Still, if the child IS of Cardassian level intelligence he has a great future as a leader of the Kazon.