At the moment the code in org.jboss.metadata.builder.jaxws.JAXWSMetaDataBuilder.addFault does not use the namespace information from @WebFault (if present) for the xml type in the WSDL schema that is generated. It is easy to change the code to do this, however I'm not sure if this would break some other use cases.
The other approach would be to use the XmlType annotation (not used at all at the moment).