WordPress plugin to disable the deletion of plugin files when running the uninstaller. Drop this in your mu-plugins directory before running the uninstaller.

disable-plugin-delete.php

<?php
/**
 * Plugin Name:  Disable Plugin Deletion
 * Description:  Disables the deletion of plugin files when running the uninstaller
 * Author:       Jonathan Brinley
 * Version:      1.0.0
 * Author URI:   https://xplus3.net/
 * License:      GPLv2 or later
 */

namespace No_Delete_Filesystem;

/**
 * Prevents the plugin uninstaller from deleting the actual plugin files.
 *
 * Works by overriding the global $wp_filesystem object with a wrapper.
 * Any call to delete a file will do nothing. Everything else is passed
 * through to the original object.
 */
class No_Delete_Filesystem {
	/** @var \WP_Filesystem_Base */
	private $filesystem;

	public function __construct( \WP_Filesystem_Base $filesystem ) {
		$this->filesystem = $filesystem;
	}

	/**
	 * Delegate everything to the wrapped filesystem
	 */
	public function __call( $method, $args ) {
		return call_user_func_array( [ $this->filesystem, $method ], $args );
	}

	/**
	 * Just pretend that deletion worked, but don't do anything
	 */
	public function delete( $file, $recursive = false, $type = false ) {
		return true;
	}

	public function override_global_filesystem() {
		$GLOBALS['wp_filesystem'] = $this;
	}

	public function reset_global_filesystem() {
		$GLOBALS['wp_filesystem'] = $this->filesystem;
	}
}

/**
 * Get the global singleton instance
 *
 * @return No_Delete_Filesystem
 */
function get_no_delete_filesystem() {
	static $filesystem;
	if ( ! $filesystem ) {
		$filesystem = new No_Delete_Filesystem( $GLOBALS['wp_filesystem'] );
	}

	return $filesystem;
}

function tear_down() {
	get_no_delete_filesystem()->reset_global_filesystem();
	remove_action( 'deleted_plugin', __FUNCTION__, 10 );
}

add_action( 'delete_plugin', function () {
	get_no_delete_filesystem()->override_global_filesystem();
	add_action( 'deleted_plugin', __NAMESPACE__ . '\\tear_down', 10, 0 );
} );