Prevent Admin users from deactivating plugins.

disable-deactivate-plugins.php

<?php 

/**
 * Prevent Admin users from deactivating plugins.
 *
 * While this will remove the deactivation link it does NOT prevent deactivation
 * It will only hide the link to deactivate.
 */
add_filter( 'plugin_action_links', function ( $actions, $plugin_file, $plugin_data, $context ) {

	if ( array_key_exists( 'deactivate', $actions ) ){
		unset( $actions['deactivate'] );
	}

	return $actions;

}, 10, 4 );