Unfortunately we didn't find a way to do this cleanly using the iis:WebApplicationExtension in WiX.
We found this post http://blogs.msdn.com/b/david.wang/archive/2004/12/02/273681.aspx that provides a VBScript for adding ScriptMaps. We edited the script to only execute the HandleListOps function (with the relevant params) so that we didn't get any issues with WScript. We then call this from a CustomAction in WiX, with the vbs file added as a Binary file.
We're aware that running vbscript custom actions from within an installer isn't ideal, but luckily we're not distributing the application externally and is only going to be used on an internal website, so the target server environment is reasonably well known.