We get pretty regular inquiries about using carbon clinchers for cross, and our answer is always the same, that we don't recommend it. The primary issue is that it's just too easy to hit the wrong root or the wrong rock and damage the brake track, but there are other things at play.
On the road, sure you can hit a pothole and if it's sharp enough and you hit it hard enough, you can damage your rim. Certainly plenty of people have dented aluminum rims on potholes and stuff (I have), but on the road you tend to have a little more latitude to avoid these kind of things, and you've got a heck of a lot more air pressure in your tire to buffer the impact. A cross (or mountain bike, for that matter) wheel is protected by a HECK of a lot less air pressure, and is subjected to a steadier stream of bigger hazards.
On the topic of air pressure, you're basically trying to run as little as possible in cross. Lower pressure gives you better traction and control. Lower pressure also gives you more vulnerability to pinch flats. Tubulars suffer pinch flats a lot less frequently than clinchers, and thus you can run them at lower pressure than clinchers. Tubulars suffer fewer pinch flats than clinchers because the tubular tire's construction make it somewhat less vulnerable to them, but mostly because the tire bed of a tubular is WAY less sharp than the brake track of a clincher.
Wider clinchers offer some means of protection against pinch flats as well. With a wider rim, the tube "muffin tops" outboard of the brake track less than with a shallower rim. There's less "tube flab" hanging out to go and get pinched. Because I was using a disc-equipped frame last year and never got to the point of making myself a disc-specific tubular, I raced all season on an aluminum clincher rear. I had one flat, which was from a sharp rock and was not a pinch flat. I rode quite a bit on single track trails last year, and just did a singletrack ride the other day on aluminum clinchers. I'm convinced that the wide rim on our aluminum clinchers prevents pinch flats, but alas the rim from last year is not in "as new" condition. Despite having never felt a brake pad, it does have minor dents and dings from rock strikes. Nothing crazy, but I still wouldn't want to expose a carbon brake track to this kind of lifestyle. Our carbon clincher rims are pretty wide, but not as wide as our aluminum clinchers, and since the brake track on the carbon rim is slightly thicker, the inner width is even less.
Carbon is stronger than aluminum, ounce per ounce, and is going to resist damage better than aluminum. A carbon rim will laugh at many rock strikes that put nice dents in aluminum rims. On the other hand, aluminum bends, and carbon breaks; when you exceed the yield point of a carbon rim, it's got permanent damage. With aluminum rims, you coerce the bend out of them, hit the spot with some sandpaper to feather out the hump, and on with life you go. Not so with carbon - you crack it, it's cracked. If the rim is badly damaged, an aluminum rim is a lot less bankroll to replace. Even with our crash replacement policy, which is as generous as we can make it, you can buy a complete new set of aluminum wheels for not a ton more than the cost of having one carbon wheel rebuilt.
Carbon rims offer some nice benefits for cross, for sure. On carbon tubulars, you get a pretty profound level of stiffness from the wheel which really lets you feel how the tire is working - nearly no feedback from the tire is lost in translation through the wheel. It's nice. But the benefits of tubular fully outweigh the benefits of carbon.
Our carbon clinchers HAVE been used for cross, by one of our team mates, who's really really really good at cross - he destroyed a clincher in a pileup early in the year last year and had to go clincher for a couple of races while he waited for the replacement tire. He did very well in the races in which he used the carbon clinchers, and they suffered no damage. It's not a case of "you WILL destroy them," it's more a case of it being a risk that we don't think is really worth taking.