Hi Markz,
when you track an email from Outlook to CRM no javascript code is executed.
You need to write a plugin, you can start from here:
http://msdn.microsoft.com/en-us/library/gg328263.aspx
and here an article to remove html tag with C#
http://hemantrautela.blogspot.com/2012/09/remove-html-tags-from-string-cnet-aspnet.html
