how to disable a class in migrate module
I'm currently using Drupal 7.22.

For my migration class, in my migrate_mypages.install file I have:

function migrate_mypages_enable() {
  Migration::registerMigration('MyPagesMigration');
}

function migrate_mypages_disable() {
  Migration::deregisterMigration('MyPages');
}


I haven't looked into the actual Migrate module, but it seems that when registering a migration in code, you have to use the full class name, whereas when de-registering the migration in code, you use only the name of your migration (machine-name).

If you are stuck with old classes, you can either add the de-register lines back in, and enable/disable your module, or, manually clear the class lines out of the table "migrate_status" in your database (as per Neograph734's comment).

As well, if you use drush, there is also:

drush migrate-deregister --orphans