How can I use a views template to modify the titles of taxonomy links?
You need to create another field with the 'path' and set this to not display by default within the views UI.

You can then get the 'path' variable in your template along with the 'title' variable and create your link using Drupals l() function.

   print l($data['rendered']['#title'], $path);


http://api.drupal.org/api/drupal/includes%21common.inc/function/l/7