If you stop the logon service it will stop it authenticated. However, it will also stop recplication between the domain controllers, so it will get out of sync and will be no good when you wan to use it as a backup.
the other option is to put it on a seperate subnet and then configure AD Sites and Services to sync between the 2 subnets. This way the computers will not us it to logon to as it is not on the local subnet.