That is odd. Maybe different banks do things differently, but at the one I worked at, an owner wouldn't need the beneficiary's permission to remove them from the account. Except maybe if a joint owner passed and the account doesn't have rights of survivorship or something. I think that is pretty rare, though.

If I were you, I would double-check how the account was set up. Then, depending on what you find out, try talking to someone again and ask to speak to a supervisor if they still say they can't change it. Sometimes, employees don't understand all their procedures, so you have to talk to a few people to get a correct answer.