Considering it's a constantly developing game, I don't feel being able to choose to refund zetas is a viable option. You had the zeta for a time and earned rewards based off of having said zeta. If you want the refund, should CG go back through server logs and refund to themselves all the rewards/resources you earned by utilizing said zeta?
You spent the resources, you earned the rewards. Just because it's not useful now doesn't mean you get to use it elsewhere. That'd be like driving a car for five years then demanding full value exchange because a newer, better car came along. Nope.
That being said; Grand Master Yoda's leadership zeta was a completely shameful move on their part. They obviously knew Bastila was incoming a few weeks later, yet they trumpeted their new Yoda rework and got countless players to bite on a completely useless zeta now.
Even if you run two very strong Jedi teams, guaranteed Yoda is not the leader on one of them. He's an asset for DPS and buffs, but not leadership.