A wordpress site depends a lot on it plugins. Sometimes a client deactivates the plugin and the site breaksdown starts malfunctioning. For this kind of problems you must inform your clients about what kind of plugin you have used and which plugins can be stopped using controls.
You can hide the links so that user can see them and this can be imposed using plugin_action_links.
One more option which can be handy is creating and Admin Overload. Here we add a role named Overlord who can perform all the activities that an admins can. To know more about the process, have a detailed look at http://premium.wpmudev.org/blog/managing-client-access-plugins/