Question: I have a remote win xp machine to which I connect via RDP. When I open a Cisco VPN connection (4.8 client) on that machine, the RDP connection drops because all traffic is routed over the VPN connection now.

Is there a way to make this work?

me => rdp => winXp => vpn => target

Answer: 
Typically the SC is on a 'proper' routable network to allow for management, if you want the SC to deal with the VMs in any way (and it's a **very** bad idea by the way) you need to put the VMs on the same network as the SC or one that is routable from the SC.
I don't think you can access the OS directly from an ESX host, and until you network those machines you aren't going to be able to run commands on them through SSH. Since you are switching IP tables off, I am assuming that you don't have a security policy in place that requires IP tables (or any firewall) is switched on before connecting them to the network.

So I suggest switching the network on, allowing DHCP to configure the IP address and DNS entries for each host and then use SSH (via a script) to do your configuration tasks.

[Functionality similar to what you are thinking of exists in Xen](http://wiki.xensource.com/xenwiki/Command_Line_Interface), although this also requires a network connection to get the commands through.