Hiding the category (unchecking the shown option) should not remove protection - it didn't do that to my "Region: Celestial" category.
I wouldn't try Knightblade's idea, because if you hide all the preset categories you automatically run into the problem he mentioned: "If you add a tag, and someone else adds the same tag, and you import that second set of stuff, you are going to have some problem because RW will see them as different tags."
If you add a new tag "Neuter" to the Domain "Gender," and you share material with three people, one of whom has also added the tag "Neuter" to "Gender," then you have problems with that one person's material because you will see a duplicate "Neuter" tag - and from what I gather, this will only be a problem with the individuals who have been tagged as "Neuter," not ones tagged with Male or Female.
However, if you delete the global domain "Gender" and replace it with your own domain "Gender" then you'll have problems with everyone you share with because you'll have duplicated one of the global domains - you'll have to find the Gender identifier on every individual you import (using the global domain) and switch it over to your "Gender" domain to keep everything consistent.
Similarly, if you delete the "Individual" category and replace it with "Character," you'll need to convert anything you import to your "Character" category - and if you share anything other people will need to convert your Characters to the standard Individual category. This will almost certainly cause more problems than adding tags to a global category.
From what I can tell Zaphod is right that adding a new tag shouldn't cause problems as long as you don't duplicate any existing global content.