Perhaps they aren’t going to make Elsa a villain, at least in the traditional sense that we’ve seen with Pan/WWW.
My headcannon? While searching for a way to find Bae years ago, Rumple destroyed the kingdom of Arendelle and trapped Elsa in the vault to ensure she couldn’t stop him. Now that she’s out, she wants to find her sister. Rumple, being that he now knows the pain of losing his son, begrudgingly decides to help Elsa as a way to redeem himself – especially after Belle finds out about Zelena.