Disable Panels Preview when adding new Panes in Layout Editor
I had same problem in one of my project. Then what I did, I added a custom code to remove all the js files except drupal core js, Panels js, Token Js, Ctools js and Views Js. And it is only for the panel pages so it solve the issue of jquery version.
We also have a drupal module jqmulti for this. But in some cases it also do not work well. That is why I removed all the unwanted js files from panel page.
Here is the sample code for this.

function custom_module_js_alter(&amp;$js){
  if(arg(0) == 'admin' &amp;&amp; arg(1) == 'structure' &amp;&amp; arg(2) == 'pages'){
    $allow = array('modules/filter/filter.js', 'modules/field/modules/text/text.js', 'modules/file/file.js');
    foreach($js as $key =&gt; $value){
      $pos =  strpos($key, 'misc');
      if(strstr($key, 'misc') == '' &amp;&amp; $key != 'settings' &amp;&amp; strstr($key, 'ctools') == '' &amp;&amp; strstr($key, 'panels') == '' &amp;&amp; strstr($key, 'views') == '' &amp;&amp; strstr($key, 'token') == '' &amp;&amp; strstr($key, 'admin_menu') == '' &amp;&amp; !in_array($key, $allow)){
        unset($js[$key]);
      }
    }
  }
}