The classes in org.docx4j.wml are generated from modified copies of the ECMA 376 schemas (ie Word 2007).
There are some minor differences between the 2007 and 2003 schemas, which will affect your application if your docs use those features.
Off the top of my head, the main thing you need to do to use docx4j to save in Word 2003 xml is to write the document out using Word 2003 namespace declarations.
We don't have a method to do that at the moment.
You'll see that SaveToZipFile
basically saves the result of calling, for each part, marshal(java.io.OutputStream os) in JaxbXmlPart
(those class names are hyperlinks...).
So you need to intercept that and translate the namespaces. Should be pretty straightforward to try out.
An alternative would be to modify the schemas (which are in svn) so that they match Word 2003, and then regenerate the classes so you use Word 2003 XML from end to end. This would be more fiddlely, and wouldn't interoperate with Word 2007.