This seems totally obvious now that we've talked about it a bit in the support forums but a staging plugin would be a fabulous addition to your plugin mix. The best integration is probably at wpengine.com but I've never liked that I couldn't push my changes back to live (have to actually replicate them).
A plugin like SitePush (http://wordpress.org/extend/plugins/sitepush/) handles it by setting up a completely different folder & database with the config files ideally residing outside of the web root.
A simpler way to go about it would be to replicate the site to a different database prefix. This would make a lot of sense for smaller WP builds and I can see the plugin having a basic vs advanced configuration.
In the end, the ability to push a site to dev.site.com (or site.com/dev in basic mode), make changes, test them, then push them back to the live site is a critical asset to any web developer or site owner. Being able to do so using the trademark GUI simplicity of WPMU - well - let's just say I think you'll find the code is worth its weight in new subscriptions.