I'm missing most of the details of what you really want to achieve, however, few considerations:
1) FYI the SAAJ MessageFactory.newInstance(soapProtocol) basically ends up doing a classloader getResource lookup. So the actual message factory being used to create soap messages is controlled by the META-INF/services/javax.xml.soap.MessageFactory file you might have in a jar archive included in your classpath. JBossWS-Native has its own implementation of SAAJ API...
2) also considering JBossWS-Native is EOLed, you should probably try JBoss AS 7 which defaults to JBossWS-CXF stack. That works with the SAAJ RI (what's in JDK), so you would most probably avoid any issue here