thanks for posting on this issue. As far as I understood, the problem comes from the maven-war-plugin that include any not-provided scope dependency artifact into the generated war archive. I see the issue of creating slim wars with that plugin is quite hot on the internet and there're probably still some bugs in Maven and its plugins to be fixed on that topic. However, I agree that the jbossws jaxws-tools maven plugin should be able to work with provided scope dependencies too. Hence I created and just solved https://issues.jboss.org/browse/JBWS-3402 . It's going into release 1.1.0.GA which is meant for JBossWS 4 usage (to be hopefully released next week).
As a workaround in the mean time or if you want to stay on JBWS 3.2.2, have a look at the war plugin documentation, there're options for filtering our stuff from the generated archive.