Not sure what you mean by deactivate the library. You do know that you can have multiple Aperture libraries on your HD?
You could leave the current library alone, create a new empty library and begin reorganizing using the new library. Once you are sure the new library is working as you'd like you could delete or archive the old library.
You could also create two top-level Folders:
- Old Scheme, and
- New Scheme.
Select your entire current organization and drag-drop it into the new Folder "Old Scheme".
Create your new scheme under the Folder "New Scheme".
When you're done, you should have nothing left under "Old Scheme". Delete the empty Folder.
Then select your entire new scheme (except for the top-level Folder) and drag-drop it on top of "Projects and Albums". You now have your new scheme. Delete the now-empty Folder "New Scheme".
This, of course, let's you access everything while you build your new scheme.