Fast Forward 2 years......November 2016 update....
In the latest version of the code , you should use com.splunk.modinput.jms.custom.handler.BodyOnlyMessageHandler , this is built in with the core release , so you don't need to do anything other than declaring this handler to be applied in your JMS stanza.
https://github.com/damiendallimore/SplunkModularInputsJavaFramework/blob/master/jms/src/com/splunk/modinput/jms/custom/handler/BodyOnlyMessageHandler.java
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