I agree with this assessment. The fact that carbon is more of an insulator means that when you brake hard, quickly dumping a tremendous amount of thermal energy into the rims, the heat dissipation through the rim material can't keep up, and you probably get very high temperatures on the braking surface. Others have mentioned a metal braking surface on carbon rims, but that doesn't really help the problem. The metal surface may be more abrasion resistant, but the core material is still carbon, and still isn't good for dissipating heat.
Based on this experience, I think the only reasonable approach to using carbon rims on a tandem is to use disc brakes. Rim brakes will probably be fine for 99% of your riding. But you'd want to avoid long steep descents at all costs. And, on any moderate descents, you'd be wondering how close to the "cliff" you are. Not worth it!
Thanks for sharing the details of this experience. It may eventually help others.