Please see http://community.jboss.org/wiki/JBossWS-SupportedTargetContainers
JBossWS-CXF 3.4.1 is not meant for running on top of JBoss AS 5.1.0. That's most probably why the server is not booting. Try starting over from a vanilla 5.1.0 and installing jbossws-cxf 3.4.0 if you need for an update.
Yes, of course the installation change some files on the server (especially installing jbws-cxf on top of an AS that includes jbossws-native), that the reason of updating ;-)
The plugin is meant for using the stack that's available. Check the way the classpath it's build; generally speaking the java.endorsed.dirs setup influences the resolution of the jaxws provider. So if that's pointing to a dir containing jbossws-native libs, the plugin will end up trying to instanciate native jaxws implementation, etc.