Javascript in textarea body

I understand that since ckeditor is javascript based running scripsts inside the textarea can cause issues.

I thought I had a workaround where I put html comment tags around script and link tags before the WYSIWYG browser loads and then before inserting into the database I remove them. This seems to work fine in FireFox but in IE CKeditor trys to load but just hangs. I also tried dynamically making the browser start in source mode, which works fine except that my end users complained that they needed to see their edits.

I also tried config.protectedSource (did not help)

Is there a workaround for this? I cannot remove the scripts because people will need to edit them in source view, but need a surefire way to make them not run and crash the browser.

Is there something in the config that I missed??? Below is an example of code getting loaded into the editor. You can see that I already dynamically applied comments around what I thought would break the editor.

Thanks!

<table align="left" border="0" cellpadding="0" cellspacing="0" width="450">
                    <tbody>
                        <tr>
                            <td align="left" height="390" valign="top"><!--<link href="/js/nivo/nivo-slider.css" media="screen" rel="stylesheet" type="text/css">--><!--<link href="/js/nivo/themes/default/default.css" rel="stylesheet" type="text/css">-->
                                <style type="text/css">
#slider { position:relative; width:440px; height:250px; background:url(/js/jQuery/loadingAnimation.gif) no-repeat 50% 50%;}
  #slider img { position:absolute; top:0px; left:0px; display:none; }
  #slider a { border:0; display:block; }                                </style>
                                <!--<script src="/js/nivo/jquery.nivo.slider.pack.js" type="text/javascript"></script>--><!--<script type="text/javascript">$(window).load(function() { $('#slider').nivoSlider({ effect: 'fade', pauseOnHover: false, controlNav: false, directionNav: false, animSpeed: 500, pauseTime: 3000 }); });</script>-->
                                <div class="slider-wrapper theme-default">
                                <div class="nivoSlider" id="slider"><img alt="" src="/images/Los-Angeles-Orange-County-Website-Designs-1.jpg" /><img alt="" src="/images/Los-Angeles-Orange-County-Website-Designs-2.jpg" /></div>
                                </div>
                                <div style="text-align: right; padding-top: 40px;"><!--<script src="/js/emailsignup.js" type="text/javascript"></script>--></div>
                            </td>
                        </tr>
                    </tbody>
                </table>