JDOM content can be attached to only one parent (Element/Document) at a time. Your response is already attached to the parent Element 'Body' in the soap namespace.
You either need to detach the response from it's parent, or you need to clone it and create a new instance..... In this case, detach()
is your friend:
response.detach();
System.out.println(new XMLOutputter().outputString(new Document(response)));
as the maintainder of the JDOM project it comes naturally to me to recommend that you use it, so take it with the appropriate level of bias.
As for an introduction/tutorial for JDOM, well, you're right, it's not fantastic, but, the FAQ is useful, and I set up a 'primer' on the github wiki here. If you have any questions the jdom-interest mailing list is active, and I regularly monitor the jdom
and jdom-2
tags here in stackoverflow.