I used to as a matter of procedure run my outboard dry when putting the boat away in Honolulu. The theory was the greater danger was leaving fuel in the system was worse for the engine, like the gunk issue reported here. Never had a problem doing this. Of course the engine was water cooled by drawing water through as it ran, so over heating should not have been a problem.
Oh yeah, water used during this process was fresh to clean the salt water from the system.