It's a Tuvix level decision I'm glad I didn't have to make. I think reuniting a child with their biological parent is a general, understandable guideline. And if you look at this clusterfuck in sequence, the first crime in this case - the illegal invasion of Bajor notwithstanding - is Rugal's abduction by Dukat's aide and his subsequent depositing in an orphanage. If it hadn't been for that, Rugal would not have had Bajoran foster parents. Who were understandably not very nuanced about the Cardassians. (There must have been a way to raise him not hating his "kind" unconditionally as he does. So they carry a small dose of guilt for this mess in my opinion.) Which led to Rugal biting Garak.

The biological dad makes a convincing case that he was fucked over. Rugal is fucked no matter what. Sisko went back to where this train was sent on the wrong track and corrected that. I can kind of see the logic of that decision. He had to weigh different factors and decided to give less weight to Rugal's wishes over the crimes that preceded him ever being in a position to express them this way.

Tough call but he (somehow, there doesn't appear to be a legal system with a metal sphere gavel and the social worker from Mrs Doubtfire presiding just yet) had to make one. And there probably isn't a right decision.