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The Graffle file format isn't very handy for anyone but us. (It is in XML, but it is just using Apple's property list DTD and is pretty grungy to read through.) One of the big things planned for version 5 is a real, good XML file format.

However, Graffle does import OmniOutliner files, which do use a very nice XML doc type. So if producing XML is easiest for you, outputting Outliner files and having Graffle open them might work best.

Alternatively, you may also want to look at the graphviz format, which is especially simple to create, and is another format that OmniGraffle can import.

If you wanted to go into more detail about what your existing XML looks like, it might also make sense to write an AppleScript that reads the XML and builds the Graffle shapes from it as well.