Rumple has been proven NOT to be Zelena’s father because she had to use HIS blood to get past the blood magic seal on his safe in the shop whereas she used her own blood to get past Regina’s blood magic.
Rumple changed the agreement with Cora to Cora had to give Rumple “his” child. Cora escaped the deal because ANY child she had wouldn’t be Rumple’s.
Rumple didn’t meet Cora until Miller’s daughter and Zelena is the older sister. Cora had Zelena before she met Rumple. Rumple kept track of Cora and Regina, he would’ve known if Cora had a child before Regina after their affair ended.
Crack theory: Zelena’s real dad is Sweeney Todd. We have had razors, shaving and meat pies linked to Zelena.