Actually the rear cylinder shutdown strategy wasn't to protect the engine, it was designed to reduce the heat that customers were screaming about to Harley. Previous versions of EITMS used a totally different strategy, namely first reducing idle speed (fewer combustion events equals less heat), then adding a little extra fuel and advancing timing 10°, and if temps still climbed the engine management system would go into what was called skip fire mode. That basically caused both cylinders to alternate skipping a combustion event by turning the injectors off at random 2 out of every 8 cycles (think of it as a misfire). That system was designed to protect the engine, and the last step didn't occur until the engine temperature exceeded 329°F. In contrast, the 2008 and later EITMS shuts down the rear cylinder spark and fuel at 287°F, turning it into an air pump that just pumps air through the head and exhaust to cool them.
If you were to remove the primary cover and watch the compensator and primary chain when the engine was only running on the front cylinder, you would see why people claim it's hard on the engine. Not as hard as dropping the clutch at 6000 rpm from a dead stop perhaps, but still not ideal.
If your desire is to protect the engine, versus just keeping your right leg and thigh cooler, a much better approach would be to install a set of fans blowing directly on the cylinder heads IMHO.
Jerry