In some cases, a vista gradebook column can't be deleted via the GUI because Vista thinks that it shouldn't be able to.
This might work in some of these cases.
Find the column in question in the SECTION_COLUMN table in the Vista database and set the inherited_fl field to 1
You can find the columns for a section with this query
The template_id is the tp part of the section url if you copy it from the My Vista page.