I believe there's no way to remove a category without direct database hackery. We didn't want to have a Meta category for Collab, but when I asked about nuking it people expressed concerns about clobbering one of the default ones (nobody was quite sure what would break). The category is here, but we set its access level so that only moderators can see it.
I also don't know what would happen to posts in a category you deleted -- even if the posts are first deleted, they still expect to be associated with a community. This would show up on profiles and in the "recent deleted posts" mod tool, for example. Deleting a category might break things there.
If you want to experiment, I would create a new category, create one post in it, get that post ID (stash it somewhere), and delete the category in the DB. If the user profile page breaks because of that post, you could assign it to a different category (with the same tag set) in the database -- this is why I said to hold onto the post ID.