Actually the solve of this problem was a bit more tricky. First of all I manually had to configure the manifest file of the package on the IS server to use the jars provided in the package abnd thus it wouldn't get in conflict with the Axis used by the IS itself. On the other hand I had to manually add the ClassLoader because WebMethods can't use META-INF based information from jar files as it seems. To solve this problem simply use:
System.setProperty("org.apache.axiom.om.OMMetaFactory", "org.apache.axiom.om.impl.llom.factory.OMLinkedListMetaFactory");
That solves all the problems.