Well, at least after watching 3×14 we can safely rule out Rumple being the father of Zelena. She needed a drop of Rumple’s blood to open his safe which had been sealed by blood magic. If she were really his daughter, she could have opened it herself, similar to how Neal was able to open his father’s hidden cabinet in the Dark Castle in 3×3. There you go. Concrete proof that Zelena is not Rumple’s daughter.
Zelena did give a few hints about her father though. He was a drunk who couldn’t hold his hands steady enough to hold a razor blade, so Zelena had to shave him herself. It’s possible she was talking about her biological father, but I’m tempted to say that she might have been talking about her foster father. In 3×13, Zelena said that Cora gave her up and that she grew up in Oz, which leads me to wonder if she was taken in by a couple from Oz.
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy