Exclude tpl files in multisite theme
Its trickier to 'remove' the template on sites you don't want it on because Drupal will always recognize the file format as a valid template and add it to theme suggestions. An easier option would be to affirmatively add it using a custom module only on the sites you want it on. For example, following this answer, here's how you would register a particular template file only on the subsites you want by just selectively enabling the module where you need it:

/*
 * Implementation of hook_theme().
 */
function YOUR_SUBSITE_MODULE_theme($existing, $type, $theme, $path){
  return array(
    'YOUR_SUBSITE' =&gt; array(
      'variables' =&gt; array('content' =&gt; NULL),
      'file' =&gt; 'page--front', // place your file in 'theme' folder of you module folder
      'path' =&gt; drupal_get_path('module', 'YOUR_SUBSITE_MODULE') .'/theme'
    )
  );
}

function YOUR_SUBSITE_MODULE_page(){

  // some code to generate $content variable

  return theme('YOUR_SUBSITE', $content); // use $content variable in moon.tpl.php template
}