Secure ArcGIS Server services are now supported in the map when you add the layer directly to the map. From the map, click Add, then click Layer from the web. Enter the URL to the ArcGIS Server service and click OK. You'll be prompted to enter a username and password. This web map can then be referenced from a template and the user will be prompted to enter the username and password. This is supported with ArcGIS Server 10 sp1 and later.
Hope this helps,
Mike