It's by no means obvious that you should or even
need to store the XML in object-form.
The real question is, first, what is the tradeoff between
the costs (speed, etc.), amount of effort breaking the XML down into objects and then storing the objects
and
storing the XML as CLOB or something instead.
If there's a need to query the stored XML with field-criteria filtering etc, then yes - XML-object-Hib-DB might be the way to go (avoid substring-SQL horrors)
If the main need is to "replay" the JMS-messaging through existing processes, there's less need for objects-on-demand.
If there's no need for granular after-the-fact field-level access to what was originally XML over JMS, why go to the trouble?
Consider the tradeoff above first. Then you can see how Hibernate helps you. Frankly, I'd use Hibernate either way - the ORM would be a lot simpler in one case vs. the other, but I see no reason not to use Hibernate either way.
You could consider JIT XML-object conversion - read the XML, run it through a JAXB, Commons-Digester etc. XML-object conversion.
Many choices, none of them obvious. It all depends on needs - actual and anticipated.