Indeed, Mentch & IITFT. Mir was in Poland before WW2. Then in 1939, it was in the Soviet zone of occupation. Yeshiva (and many others both from the Soviet and German zones) fled to Lithuania that remained independent until occupied by Soviets during summer 1940 – and Sugihara continued writing out visas until Soviets forced Japan to recall him.
It is clear from a question posed to R Grozdenski at the time – who should use the visas – that they were afraid of Soviets. The question assumed that senior Rabbis would be immediately killed, while younger ones will lose their children to anti-religious education.
you need to look at the events with the view of people at the time, rather than with hindsight:
1) Perception which plague was more dangerous depended somewhat on the locale and personal history: those who had experience personally, or in a family, with Soviet oppression, or who had property or involved in religious and political activity – were mostly more afraid of Soviets, except those who were involved in communist political activities who were more afraid of Nazis.
2) Experience of WW1 in that area was of awful Russian army and disciplined German one. Read Elie Wiesel, among others – even in 1944 Hungary, many people relied on that history.
3) At the time, Soviets were running murders and labor camps for 20 years. Nazis, up to invasion of Poland, had pretty benign detention camps in their own country from which people were often released…