I tend to agree with you, but in the ToS it is fairly clear that SG/Zynga own everything in the game, everything you purchase with cash or gems belongs to them, and you are not to transfer them to anyone else. With that in mind, I don’t think there is anything legally preventing them from transferring an alliance from someone who paid gems for it to someone else.
With that in mind, I would have no problem with the alliance being transferred to the longest standing active member, and either the gems being refunded to the founding leader’s account or the new leader paying 50 gems to be given to the founding account.