User errors with post categories

Question in brief:
I’m looking for a way to eliminate problems caused by users checking the wrong category checkboxes (controlling posts that appear on the front/home page as “Featured” or “Headline” posts) in the new/edit post interface.

The details:
I have some sites using the “Arthemia Free” theme. For the front page, this theme uses posts categorized as “Featured” and “Headline” posts to create a nice display. The sites are non-profit sites administered often by non-technical users. They sometimes check or uncheck the “Featured” or “Headline” categories not realizing that this will completely mess up the appearance of the front page.

So I’d like to come up with a solution to this problem …either by manipulating the categories that are offered for them to check for each new post (or edited post) or perhaps by using a custom taxonomy to specify this “Featured” or “Headline” post (Although I haven’t ever worked with custom taxonomies).

I can see that the code in:
include/template.php:wp_terms_checklist()
and the code calling it in:
include/meta-boxes.php
…is not simple code and would not be very easy to alter so I’m looking for advice from someone who has a high-level view of wordpress code and might be able to suggest a better approach.

-Patrick