On the clean up page shown after disabling a module, the admin user is invited to disable possible orphaned dependencies or leave them.
This is done by checking modules and clicking 'Disable selected modules.'
This feels really counter-intuitive, as every else in Drupal core or features you check things you want to keep, not things you want to remove.
This page should match that -- keep the checkboxes but label the column 'Enabled' like on module admin, and change the button to 'save settings'. To make it clear what is going to happen, the boxes should probably be initially selected -- add a tableselect checkbox at the top to allow quickly deselecting all the modules listed.