This is a really bad design. A) SoapRPC has been recognized as having major interoperability issues for about 5 years now and B) Sending an XML document as a parameter instead of using a document/literal message with a properly designed schema has many, many limitations such as inability to validate the XML document requirement to encode the XML as you have noted and inability to transform the request easily when intermediaries such as ESBs are in use.
Redesign this using best practices to avoid future issues with interoperability and usability.
Mark
#Flow-and-Java-services#webMethods#Integration-Server-and-ESB