Mad Max

This plugin has its the_post_thumbnail function. Just look at point 4 in “installation” section.

Vijay, is quite common for complex plugin to have a “uninstall feature” in their options page. WP can’t be aware of all the db entries created and managed by the plugin so it can’t take a general approach to clean those entries. It only do what it’s ever safe: disable and delete plugin files.
On contrary, a plugin developer knows exactly what to remove when you no longer need his plugins.

Have you check the “remove Redirection” option at the bottom of the Options Page?

It should remove everything concerning the plugin.

A little update to narrow the selection of dom elements to the images in the posts content only. I’ve supposed every theme has a “entry” class on div containing posts (like default theme has), so:

jQuery(document).ready(function() {
	var items = jQuery('div.entry a').filter(function() {
			return jQuery(this).attr('href').match(/\.(jpg|png|gif)/);
	});

	if (items.length > 1){
		var gallerySwitch="[alltogethernow]";
	}else{
		var gallerySwitch="";
	}
	items.attr('rel','zoom'+gallerySwitch);
	jQuery("div.entry a[rel^='zoom']").prettyPhoto();
});

This resolves potential problems with linked images on other parts of the page like in footer or sidebar(s)

I think there’s no need to use a plugin in this case. A manual approach should avoid problems with updates of WP and/or other plugins.
To use pretty photo library without a plugin just link css and js files in your header.php

<link rel="stylesheet" type="text/css" href="<?php bloginfo('template_directory'); ?>/prettyPhoto.css" /><br />
<script src="<?php bloginfo('stylesheet_directory'); ?>/js/jquery.prettyPhoto.js" type="text/javascript"></script><br />

or use a hook in your functions.php and load these files only where needed (i.e.: if (is_single() | is_page() | is_archive() ) -> load PP ).
Then add the lines below to jquery.prettyPhoto.js or to a new js file that you have to include as well:

jQuery.noConflict();
jQuery(document).ready(function() {
  var items = jQuery('a').filter(function() {
    return jQuery(this).attr('href').match(/\.(jpg|png|gif)/);
  });
  if (items.length > 1){
    var gallerySwitch="[alltogethernow]";
  }else{
    var gallerySwitch="";
  }
  items.attr('rel','zoom'+gallerySwitch);
  jQuery("a[rel^='zoom']").prettyPhoto();
});

It simply checks for every <a> tag linking an image and adds the correct rel to it, making a single photo zoom or a gallery.