I've looked at both JBoss and Hibernate source, and I am thinking the quick answer is NO. At least in JBoss 4.0.3.
Currently, the JBoss Hibernate MBean uses a Configuration object to initialize the session factory. In order to support annotations, it will need to use an AnnotationConfiguration object for initialization. It will also need to add some facility through the MBean's attributes to add the annotated packages and classes.
So, for those using JBoss 4.0.3, wishing to try out annotations without resorting to EJB3, it looks like JBoss' Hibernate session mgmt cannot be used.