Just thought I'd drop a line seeing as though this thread is somewhat new.
I had the same problem concerning POSTS. There were a few posts in a category that I wanted to exclude. I FOUND A WORK AROUND!
To exclude individual posts in a particular category you first need to create a new "dummy" or empty category and call it something you will remember. I called my newly created category "nrelate exclude". Now, go to your nrelate dashboard and click the check box to exclude the category "rnrelate exclude" under Exclude Catergories. Now you can go to the posts you'd like to exclude and add them to the "nrelate exclude" category, so now they are associated with two categories but one is being excluded.
This works because of the way nrelate caches the pages. It clearly says that if a post belongs to two categories and one of those categories is being excluded, that post will not be included ANYWHERE!
Hope this helps. It did for me!