Hi Mike,
Are you using ArcSDE 10? In 10, you are supposed to be able to kill direct connections easily. Say, if you use SQL Server, you can do it like this,
sdemon -o kill -t all -i <direct connection info> ....
If you use sde schema, you must grant sde user more privilege - processadmin server role.
All these are in the new ArcSDE Administration Command Reference.
Thanks!