This python script should work to set the permissions appropriately. Just swap out the path to your server connection info, FDS name and username.
Hope this helps,
# Purpose: Change user privileges on a dataset
# Create the Geoprocessor object
gp = arcgisscripting.create(9.3)
# Set the name of the feature dataset, feature class, or table to change privileges on.
objName = 'ADMIN.FDS'
# Set the name of the user or role to grant privileges to.
# Process: Update user privileges
gp.ChangePrivileges("Database Connections/Connection to Server.sde/" + objName, username, "GRANT", "GRANT")
# If an error occurred while running a tool, print the messages