There is a difference between deactivating the plugin and uninstalling it. The plugin gets deactivated if you do so on the plugins page or if you simply delete the plugin files via FTP. No uninstallation tasks are performed then, so you can activate and deactivate the plugin as you want without losing the plugin’s settings.
If you deactivate the plugin und have gravatars turned on, they will again show up for everybody, even those commenters and users who opted out of displaying gravatars. If you changed the default avatar to one of the new local avatar images, the gravatars will not be displayed until you change the default avatar image back.
