There's a way to do this at the web app level, but not just for a site.
(not that I know of)

Couldn't you just break permission  inheritance and then create/assign your
own groups?

So far as I know, site  collection administrators (if that's what you mean by
"root administrators") cannot be barred from any site within the collection.

You can remove the site  collection administrator from having access to the site.
But you can't keep them out. They can always add themselves back in and give
themselves any rights  they want to.

1. First, create  a custom permission  level at the site  Collection level. (Site
Settings, Advanced Permissions, Settings, Permission Levels, Add Permission
Level)

1a. If you do not see the Settings option on the tool bar, then the site is
inheriting from an ancestor. Choose Actions, Edit Permissions. Then repeat step
1

2. Choose the desired Base Permissions.

3. Click Site Settings, Advanced Permissions

4. Click on the [Site] Owners group. Clear the Full Control box and check Read

5. Click on the [Site] Members group. Clear the Contribute box and choose the
level created in step 1.