Excluding Categories in post-new.php?

I’m currently using WordPress as an intranet solution for a company of about 100 people. It has two sections: a knowledge base section for HR policies and whatnot and a more typical blog set-up. These are based off of categories, with certain ones included or excluded based on what the reader is trying to access.

I used the Admin Menu Editor plugin to modify the admin section so that when users log-on, they’re presented with two distinct sections. It’s just cosmetic, but it seemed to help people understand that one area is different from another (even though they’re using the same page to add new posts).

So, here’s my problem.

90% of the users are only going to be using the blog section, which means that they don’t need to see the categories for the knowledge base side. In order to clear up confusion and avoid clutter as the knowledge base expands, I want to make a custom post-new.php with those categories excluded (or, better yet, the blog parent category included only). Or, alternatively, something similar that would get the job done. A plug-in or functions.php solution would be nice.

I can’t use a custom taxonomy because I need to use the Subscribe2 plugin to send e-mail updates when posts are made and that doesn’t work with taxonomies, as far as I know.