After looking around for a long time, I found out how to turn off the ctrl-alt-del.
Go to the FreeNas UI:
System->Tunables
Add an entry:
Variable: kern.vt.kbd_reboot
Value: 0
Type: sysctl
Now the ctrl-alt-del won't reboot if you hit it accidentally when your KVM is switched to the wrong system and you are trying to log into Windows. Hope this helps someone else out there.