How do I clean cached paths to modules?
The best way to do this is to disable the module, remove the '.old' folder and then re-enable the module. Unless disabling the module is destructive, this is the course of action I would recommend.

Otherwise you need to call registry_rebuild, though as you've realised you can't do this from a module because your site won't bootstrap. There is drush command made just for this case which you can find at https://drupal.org/project/registry_rebuild

If none of this works, you will need to manually edit the database ; you will need to manually edit the 'system' table and clear the system cache. Not recomended.

Whichever option you go for, make a backup of your database first!