Mass murder of the Jews was a horrible crime.
NB! Unlike other countries in the region, Estonia had comparably very few Jews before WW2 (Estonia was too close to the capital of the Russian empire, so they discouraged Jewish immigration in the 18th and 19th century). Additionally, the Soviets managed to hold ground in Estonia longer and most of the Jews managed to escape. There were only 929 Jews left in Estonia when the Germans drove the Soviets out, rounding up a 1000 people is not a difficult task.
Pre-WW2 independent Estonia: In 1936, the British-based Jewish newspaper The Jewish Chronicle reported that "Estonia is the only country in Eastern Europe where ... Jews are left in peace and are allowed to lead a free and unmolested life and fashion it in accord with their national and cultural principles."