How to prevent Tor from starting automatically on Ubuntu server?
This is quite confusing. But generally you can edit /etc/default/tor and change RUN_DAEMON="yes" to RUN_DAEMON="no". Now Vidalia should start its own tor and tor should not start at startup.
Small update. Since 15.04, Ubuntu uses systemd instead of upstart by default so now to disable tor on startup we should run:
sudo systemctl disable tor.service