Add the following script to your page somewhere BEFORE the script that  
loads MathJax.js:
	<script type="text/x-mathjax-config">
	MathJax.Hub.Register.StartupHook("MathMenu Ready",function () {
	  MathJax.Menu.ShowSource.Window = function () {};  // don't open the  
Show Math window
	  MathJax.Menu.ShowSource.Text = function (text,event) {
	    ... your code here ...
	  };
	});
	</script>
Note that I have disabled the routine that opens the window used by  
the current ShowSource.Text function, so you won't get an unwanted  
window.
Add your code in the place indicated.  One reason that MathJax uses a  
separate window is that it is then easy to "select all" and copy the  
contents of the window.  That is not so easy to do with a div.  You  
might consider setting the selection to the contents of the div so  
that is is pre-selected when the source is shown.
Davide