Loading module-related files only on certain pages
You should use hook_js_alter() within template.php

function yourthemename_js_alter(&amp;$javascript) {
  if ('this is true') {
    unset($javascript['sites/all/modules/chosen/chosen.js']);
  }
}


I'm wondering if either solution will result in caching issues though.  If I may: I would first try to figure out why my JavaScript collides with the module and fix it there.

You can also use the hook within a custom module if you already have one that relates to what you're trying to accomplish here.