You are putting the issue in terms which uses one occupation and set of crimes to justify another.
It is not a question of justification but of explanation.
Justification of a particular act is a moral or legal issue, which is not what this discussion is about. Understanding of a historical event requires an investigation of the reasons why it happened, not a moral or legal evaluation of it.
You seem to be suggesting that it should be recognised that, for example, participation in the slaughter of Estonian Jews should be seen essentially as a reaction to the Soviet occupation in 1940. Needless to say, this would be completely unacceptable not just to Russia, but to everyone else as well.
That is precisely what I am saying. If the Soviet occupation of Estonia had never occurred, and Germany had invaded an independent country, then it is most likely that there would have little if any tendency by ethnic Estonians to collaborate with the German occupiers in the killing of the Jewish minority in Estonia or in other places.
The Jewish minority in Estonia was tiny, and did not play a major role in the country. There was no previous history of conflict between Jews and ethnic Estonians, unlike the situation in many other parts of the former Russian Empire. Prior to the Soviet occupation of 1940, there was no reason for ethnic Estonians to have any animus against the Jewish minority.
It was the historical fact of the Soviet occupation and the highly visible collaboration of elements of the Jewish minority with it that created an anti-Jewish sentiment among the Estonian people, which was strong enough in the case of some of them to induce willing collaboration with the German occupiers in the massacre of the remaining Jews in Estonia and in some neighbouring areas.
The above interpretation of the historical data may be unacceptable to Russia and to "everyone else" (read Qvist), but it is a common human failing to refuse to accept facts that one finds unpalatable.
The above interpretation is also quite separate from the question of whether certain actions by Estonians who collaborated with the German occupiers were criminal. That is an issue of legal and/or moral evaluation, and not one of understanding the reasons or motivations for historical events.
The attitude of ethnic Estonians in 1941 to the Jewish minority in their country might well be compared to that of Poles or Czechs in 1945 to the ethnic German minority in their respective countries. Poles and Czechs had a very negative view of the ethnic German minority because of the very visible collaboration of elements of it with the German occupation of their countries, and fully agreed with the punishment of the entire minority once the German occupiers had been driven out. That punishment took the form primarily of expulsion, although there were cases of massacre of members of the German minority; nevertheless, the motivation for the participation by Poles and Czechs in anti-German actions in 1945 were exactly the same as the motivation for the participation of Estonians (and Latvians and Lithuanians) in anti-Jewish actions in 1941.
Obviously not all the ethnic Germans of Poland and Czechoslovakia were guilty of collaboration and deserved their punishment. In like measure, not all the Jews of Estonia were guilty of collaboration and deserved their punichment. But in both cases, the whole population suffered because of the deeds of a part of it.
Secondly, even those who don't might take note of the fact that there was an intention to germanize the Estonian nation in its entirety. Such was the rewards of having a "high racial value" in the harebrained hierarchy of nazi lunacy. And I somehow doubt many Estonians look kindly on the notion of being promoted to real Germans and putting their slightly embarassing estonianness behind them.
Estonia had for many centuries been part of the Baltic cultural sphere, linked to the Finland and the Scandinavian countries. That sphere had strong connections to Germany and was influenced by German culture, due to the role played by Germans in initially bringing European civilisation to Scandinavia and the Baltic area, and later to the integration of the sphere into the economic community represented by the Hanseatic League. The integration of Estonia into the Balto-Scandinavian cultural sphere is shown by its adherence to Lutheranism, a cultural identity it shares with all the Scandinavian countries and with much of Germany.
For the above reasons, Estonia is culturally quite close to Germany and Germans, far more so than to the Russian cultural sphere, which is completely alien to it. The German language had been spoken in Estonian towns for centuries, and had been the language of culture and learning; Dorpat University for example had always been German-speaking.
It is a fair bet that if Estonians had been faced with the alternatives of Russification and Germanisation, they would have chosen the latter as the more palatable, and more compatible with their own culture and history. They had been subjected to heavy-handed Russification in the last decades before the First World War, and they had not liked it one bit.