I have Pathologic installed and it is working great from normal links in a document, but for anything that points to the file system ( img src for example) I can't get it to not use ?q= in the url.
You could alternatively use the scanner module or export the DB and use a text editor to replace the domains. Therefore getting rid of pathologic.
If you know how to write a custom module, you can implement hook_pathologic_alter() and tell Pathologic to not modify certain paths. See pathologic.api.php for examples.