I don't think the uninstaller will uninstall saved games unless you specify you want to get rid of them? But just in case, browse to the following folders depending on what operating system you use:
Windows XP
C

Documents and Settings\account\My Documents\Sports Interative\Football Manager 2008\games
Windows Vista
C

Users\account\Documents\Sports Interactive\Football Manager 2008\games
In that folder are your saved game. So copy those files to another folder somewhere else, such as on your Desktop, then uninstall the game. Reinstall the game and if the games have been removed just move them back to the folder above when/if the game recreates it, and you'll be all set.