Alter Commerce Line Item Order Edit Form
If you want to add an editable column, you cannot do that just through the theme layer (though I think the same would hold true even for a non-editable column). Instead you need to alter the form element that gets created, even if it's just through an order edit form level alteration. First you need to create the elements you need in the form array and then you can override the theme function to ensure they get rendered into the table in the right column.

You should also look up documentation on how to override theme functions in general. You shouldn't need to alter the theme registry, just place the theme function in your theme's template.php, copy the functionality of the default theme function, and alter it to your need.