How to avoid Pathologic module to change a javascript src value?
You can try adding Javascript in your template files by using

&lt;?php
drupal_add_js(drupal_get_path('theme', 'mytheme') .'/mytheme.js');
?&gt;


also this works in modules etc as explained here: http://drupal.org/node/304255

sometimes it is comfortable to add whole JavaScript inline:

drupal_add_js('jQuery(document).ready(function(){   
   // Your stuff
   })      
', 'inline');


Hope that helps avoid that module behaviour.