One approach would be to first turn both XML files into Canonical XML, and compare the results using diff. For example, xmllint can be used to canonicalize XML.
$ xmllint --c14n one.xml > 1.xml
$ xmllint --c14n two.xml > 2.xml
$ diff 1.xml 2.xml
Or as a one-liner.
$ diff <(xmllint --c14n one.xml) <(xmllint --c14n two.xml)
