I'm setting up a physically isolated Tor system (with one computer serving as the workstation and another as a Tor gateway), ...
I don't know what your "physically isolated" refers to, but since you have a work station connected to a Tor gateway I would assume that you plan to use the workstation to access the internet through the Tor gateway. In this case you have no "physical" but only a (weak) logical separation.
In any case a common "worm" propagating through the network could usually already prevented if you don't offer any services on your system, that is you have only outgoing connections. But since you probably want to access the web and maybe read email you should worry less about hackers trying to attack your system from outside, but more about attacks you are implicitly inviting to your system, i.e. drive-by-downloads, malvertising, phishing mails with infected attachments etc. There is no absolute protection against this, but using a read-only system (like a Linux live-ISO distribution) can help, especially if you restart to get a clean version before doing any sensitive activities.
Would something like a networking worm be able to bridge the 'air gap' between the two computers and compromise my identity,