First of all, Class::DBI will be getting support for composite keys soon. Join the mailing list if you're interested. SPOPS already has support for composite keys.
Keep in mind that when Class::DBI's built in relationships fail you, you can always add a method to it that runs an arbitrary SQL query and returns one or more objects. That might be the best thing to do in your case. There will always be things that an O/R mapping tool doesn't handle well, and that's when the ability to add hand-coded SQL transparently becomes important.
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