You are close. Try this instead:
package Page;
__PACKAGE__->has_many(columns => 'Column');
package Page_column;
__PACKAGE__->has_a(page_id => 'Page');
__PACKAGE__->has_a(column_id => 'Column');
package Column;
__PACKAGE__->has_many(pages => 'Page');
And if your immediate question is "Why can columns have multiple pages", then you need
to go back to your 1NF 1:N design, like kal suggested. Your second example is what i call a cross
table, and the tables on the ends are the "many" relationships.
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