An application that is in the login items will bounce in the dock so how would expect a user not to know it is running.
As you can start n stop a vpn service via the command line you could configure a launchd process to start a script.
To easily create launchd processes you can use
lingon
This hint
Accessing a VPN (PPTP) via the command line could be used to write a bash shell script.
Or you could install a 3rd party command line vpn client see this hint
Install vpnc as a replacement for the Cisco VPN client
This would be done in the background.