Yes, as per OpenGL 4.5, it is legal to delete it after you unbind the VAO.
2.6.1.2 Name Deletion and Object Deletion
If an object is deleted while it is currently in use by a GL context, its name
is immediately marked as unused, and some types of objects are automatically
unbound from binding points in the current context, as described in section 5.1.2.
However, the actual underlying object is not deleted until it is no longer in use.
This situation is discussed in more detail in section 5.1.3.
5.1.2 Automatic Unbinding of Deleted Objects
When a buffer, texture, or renderbuffer object is deleted, it is unbound from any
bind points it is bound to in the current context, and detached from any attachments
of container objects that are bound to the current context, as described for DeleteBuffers, DeleteTextures, and DeleteRenderbuffers. [...] Attachments to unbound container
objects, such as deletion of a buffer attached to a vertex array object which is not
bound to the context, are not affected and continue to act as references on the
deleted object, as described in the following section.
5.1.3 Deleted Object and Object Name Lifetimes
When a buffer, texture, sampler, renderbuffer, query, or sync object is deleted, its
name immediately becomes invalid (e.g. is marked unused), but the underlying
object will not be deleted until it is no longer in use.
A buffer, texture, sampler, or renderbuffer object is in use if any of the following conditions are satisfied:
- the object is attached to any container object
- [...]
So either it's an AMD driver bug, or the situation is not as you describe.