I was always mindful of Sisko's and Picard's differing decisions.
Here, Sisko has a Cardassian child raised by the enemy and ultimately returns the Cardassian to his home.
Picard has a human child raised by the enemy in "Suddenly Human" and tries to return the child to his home... but then stops and lets the child remain with the only family he's ever known.
Sure there are differing Cardassian, Human, Bajoran values involved, but it's a very similar situation and the two captains come to opposite conclusions. Interesting.
As I said in my original post, I can't see any one of them as being "wrong" in ruling as they did, even if it was differently. However you choose it's going to break a family pretty much.
As Laser Beam suggested, there is the psychological abuse even if it's passive, to factor into the situation. The boy -did- clearly hate Cardassians and that had to be some sort of internal hell for that. It could be that maybe Rugal's only way to find some sort of peace is to come to understanding his own heritage.
In Suddenly Human, they did everything they could to reawaken Jono's humanity. Pa'Dar never really got a chance to expose Rugal to Cardassian values at all. Certainly Jono didn't hate humans and their existence even if he considered them adversaries and culturally weak.