Sorry that happened to you! You can select all bones in setup pose, ctrl+c (cmd+c on Mac), go to animate mode, choose local axes, ctrl+v to get the same pose. This copies bone transforms but won't copy things like path constraint settings, etc.
It's true a way to lock the setup pose would be helpful to prevent accidental changes. We'd need some popup messages when you tried to modify it, else it could also cause confusion. There are many ways to modify the setup pose (it's more than just bones), so making the changes to support such a feature is not trivial.