I recommend fixing your JavaScript. In the long run you'll save yourself a lot of trouble.
If your dead set on leaving your script as it is, you can use the X-UA-Compatible meta tag (see META Tags and Locking in Future Compatibility). That should make your JavaScript work (no guarantee!).
If you want to set it at run time you can declare it on your page:
<meta id="comp" http-equiv="X-UA-Compatible" runat="server" />
and set it in the code-behind
comp.Content = "IE=EmulateIE7";
Other browser simply ignore the tag however, so you can just put it on your page like this:
<meta http-equiv="X-UA-Compatible" content="IE=EmulateIE7" />