The Icelandic writer and historian Snorri Sturluson (1179-1241) comes to mind. He wrote several sagas and the Heimskringla, the history of the Norwegian kings at a time when the Norwegian monarchy was seeking control of Iceland. Snorri may have written Heimskringla at the request of the Norwegian king, but the final work may have been regarded as too full of praise of Icelandic independence. Snorri was assassinated, presumably by the king's agents.

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Perhaps we can also give a moment to remember Marc Bloch, the famed medievalist who joined the French resistance only to be captured and shot in 1944. Not persecuted for being a historian, but a historian who was killed for being a French patriot. As far as I am concerned, he should be regarded as the patron saint of historians, and we should all be so lucky to be able to say we risked as much for such a significant cause.

Thanks. Here's what I compiled from Google. Those more familiar with these may comment, hopefully their memories tickled.

1. Roy Medvedev, Soviet historian persecuted for exposing Josef Stalin's crimes in his study 'Let History Judge', was re-admitted to the Communist Party after 20 years. I wonder whether he was forced to recant, or whether his history was accepted and canonised?

2. Sometimes historians can be persecuted for nationalism: Support for nationalist leaders began to grow in early 1990 under the influence of the nationalist campaign rhetoric of Franjo Tudjman and his Croatian Democratic Union (HDZ) leading up to Croatia’s first free elections in April. Tudjman, a former Yugoslav army general and revisionist historian persecuted for nationalism in the 1970s, downplayed the crimes of Croatia’s WWII state, the NDH, led by the fascist Ustaše, made anti-Serb (and anti-Semitic) statements, and courted the sizeable Croatian émigré community (including many extreme nationalists and, reportedly, Ustaša veterans), which eventually bankrolled his campaign.

3. Eusebius also known as "Father of Church History" lived in Palestine in 296 AD, when Diocletian's army passed through the region (in the Life of Constantine, Eusebius recalls seeing Constantine traveling with the army.) The New Testament is a collection of writings and letters written by apostles of Christ, or written under the direction of them. During the lifetime of Eusebius (A.D. 264-340, a church historian persecuted for his faith and endurance to Scripture) the books were compiled into what we know today. He became the chief religious adviser for Emperor Constantine who accepted Christianity and had 50 copies (hand printed) made for the churches of Constantinople. In 397 A.D. those 27 books were adopted unanimously & formally at the Council of Carthage as the New Testament. He wrote several histories of Christian martyrs. Following the publication of the second persecutory edict of Diocletian, prisons began to fill—the underdeveloped prison system of the time could not handle the deacons, lectors, priests, bishops, and exorcists forced upon them, and thus crowded out ordinary criminals.

4. LISKE, KSAWERY (1838-1891), historian. Persecuted for his patriotic Polish activities in Great Poland (Wielkopolska). He specialised in 16-th century Polish history. Liske established the Polish Historical Association and its organ, Kwartainik Historyczny (Historical Quarterly).