I'd recommend using an XML parser to validate the output instead of doing textual comparisons. If you're going to be parsing the xml to re-order it anyway, you may as well just do the comparison using XML tools.
Edit:
Attempting to control the generated XML by manipulating the Java source code order seems like a fragile way of doing things. Granted, this is for testing only, so if something breaks the code might still work properly. People change source code order all the time, sometimes by accident, and it will be annoying or a subtle source of problems if you have to rely on a certain ordering.
As for ways of comparing the XML data using XML tools, I've never personally done this on a large scale, but this link mentions a few free tools. For me the extension to JUnit that provides XML-related assertions would be my first step, as that could integrate well with my existing tests. Otherwise, since you're mainly looking for exact equivalence, you could just parse the two XML files, then iterate over the nodes in the 'expected' file and see if those nodes are present in the 'actual' file. Then just check for any other nodes that you don't expect to see.
