I've never understood why the commanding officer of a Federation starbase had any authority in deciding a custody dispute between Bajoran and Cardassian citizens. Rugal was a Bajoran citizen and lived on Bajor; this dispute, from a Federation POV, should clearly have been kicked over to a Bajoran court to decide.
Meanwhile, anyone interested in Rugal's story should pick up the DSN novel The Never-Ending Sacrifice
by Una McCormack. It tells the story of Rugal's life on Cardassia throughout the remainder of the series.