If you use a custom plugin to store all your theme functions, you dont want a user to deactivate it. Add this to functions.php or your custom theme plugin to hide the "deactivate" link for your selected plugin.

hide_deactivation_link.php

// Disable plugin deactivation
add_filter( 'plugin_action_links', 'slt_lock_plugins', 10, 4 );
function slt_lock_plugins( $actions, $plugin_file, $plugin_data, $context ) {
    // Remove edit link for all
    if ( array_key_exists( 'edit', $actions ) )
        unset( $actions['edit'] );
    // Remove deactivate link for crucial plugins
    if ( array_key_exists( 'deactivate', $actions ) && in_array( $plugin_file, array(
        'plugin-folder/plugin-name.php'
    )))
        unset( $actions['deactivate'] );
    return $actions;
}