Unfortunately, the racks aren't designed for the bike to be turned around (so that the arm could go over the rear wheel). Even it would provide enough support, the arm would dig into the rear stays and scratch up the frame (instead of the fork).

The inner tube idea is interesting, but I fear the rubber would be a little too thin; maybe doubling it over would work, or carrying a small piece of car tire.

I have a steel fork on there now, which has a couple of deep scratches from the arm. It's fine structurally, but I'd prefer to avoid the damage altogether.

I agree that carbon is not ideal for a commuter bike, but I also race cyclocross on the bike..