As far as I know there is no built-in way to Mock a static extension method. This it true with Moq, and I guess same for RhinoMock. Of course you can create wrappers etc, but I don't think there is built-in way. That's probably why your code hitting the real extension method even through it has been stubbed out.
public static bool IsRegistered<T>(this IUnityContainer container)
{
Guard.ArgumentNotNull((object) container, "container");
return UnityContainerExtensions.IsRegistered(container, typeof (T));
}
See also this relevant post.