Far for me to question a Dayan. But if a Dayan really said that a woman who is unhappy in the marriage situation and is not going back under any circumstances must say with her husband even if its beyond repair and wont go back. The Dayan likely did not hear all the facts or was unwilling to hear all the facts. You should seek another Dayan in that case.
There certainly is room according to many for appeals in Halacha. The Beis Din in Israel accepted it when the British mandated it in order to accept Beis Din decisions and the RCA also allows appeals so there is certainly more than enough room to allow it.