Hmm, and in actuality, I think this problem occurs when you use Stand Alone as well (for specific services like Time Machine).
One of the simplest options would be to configure things such that your servers and workstations are on different subnets, but are still routable to each other. This will erect a wall between the two where normal IP traffic can reach, but not UDP multicast.
Another option is to cripple Bonjour on the server so that it can't advertise any services, but that's probably gonna be painful to maintain and manage.
A third option is to find out if the launchd config files include information about being exposed via Bonjour (they might by having launchd cause the broadcast of the http service, for example). Edit them to not register the service on the network. You will likely need Bonjour Browser and some patience for this one to work, and you'll need to remember what you did in case an OS update undoes it for whatever reason.
EDIT: And it might not be terrible to setup the machines this way, if it lets you use a network account for your admin account. That would simplify your administration a bit by being able to create a "Workstation Admin" account in the directory and make it admin on all the boxes when you bind on install. Just a thought.