I would quit using a shared drive for shared editing. Go with a proper version control system and personal work spaces. Shared work spaces lead to all sort of issues including lost changes.
There is no reason to have all the sites checked out all the time. Checkout the sites you need and remove the related work space when you are done with the site. Your work flows will need to change accordingly.
I'll avoid repeating a lengthy answer. This question is similar to: http://programmers.stackexchange.com/questions/120613/what-version-control-system-can-manage-all-aspects/120620#120620