I am not sure why you exclude such reasons for publishing under a pseudonym as "fear of prosecution"... Andre Bloch used the pseudonyms Rene Binaud, and Marcel Segond during the German occupation of France. He was a Jew, and confined to a mental asylum at that time.
Joseph Bernstein published a paper under the pseudonym "Yantarov" (which is derived from the Russian translation of the German word "Bernstein" which means "amber"). At the time of writing he was an "otkaznik", a person waiting for permission to emigrate from the USSR, and a paper under his own name would not be accepted.

