It took a bit of hunting so I thought I should post it up for next time.
To get the Form version of the Infopath template use the following code:
this.Template.Version
Here's a sample of what I did:
XPathNavigator nav = this.CreateNavigator();
string formVersion = this.Template.Version;
nav.SelectSingleNode("/my:FormVersion",
this.NamespaceManager).SetValue(formVersion);