Class::DBI's Documentation:

Consider the case of Films and Actors, with a linking Role table. First of all we'll set up our Role class:

        Role->table('role');
        Role->columns(Primary => qw/film actor/);
        Role->has_a(film => 'Film');
        Role->has_a(actor => 'Actor');
[download]

I merely used the documentation, and it worked; but you're right with the id as new primary key, and Class::DBI workes as it should with this data-definition and All instead of Primary. (Tested using innodb, foreign keys were in effect :-)