Not wanting to scare you but the most ingenious virii do not install one thing on the harddisk, they stay in RAM as long as the machine is on.
You want to run it from a usb key rather than a harddisk. What's the difference? You can also wipe out your harddisk everyday if you have some time to waste...
Or maybe your talking of a writeprotected stick, which is like running it from the CD?
In this case, no file will be altered ok. No write possible..
Still your personnal information (from your 2nd stick or whatever writeable storage including RAM) can be extracted/modified
And your machine can still be used as a relay to attack others.
In theory, I'm not sure there is an advantage of such system.
In practice, unless you have some very interesting information on your system, most people only get hit by automated tools (with no AI behind) and they might fail with your setup if write access to / is disable.
If also you are sure that your second usb stick cannot run binary (by using special mount options) then it will be impossible for the attacker to leave a backdoor so that he comes back later if you have patched the first breach.
Being paranoid a bit?
