If it were me and I was worried about malicious mischief on the web I would
simply (as you stated) run two hard drives making sure Ubuntu is the Master and
Windows is the slave. Make sure you fix the jumpers on the hd's so that occurs.
Go into the bios and make sure the machine boots to the cd-rom drive first and
Ubuntu second. Drop your Ubuntu install disk into the cd-rom drive. Shut the
machine off. Put it back on and the machine will boot to the install disk and at
the end of the installation the grub will see the Windows drive and your worries
of viruses spreading to the Ubuntu disk are over. If you're still worried you
can always grab ClamAV from the synaptic package manager and install that. Now
you have several different ways to do your thing.