The Germans most certainly did try to overthrow a Baltic government in the interwar. In fact, they temporarily succeeded: the Latvian government was overthrown by the Germans in April 1919 (the "Liepaja Putsch") and replaced by a reactionary puppet regime under the collaborationist Andrievs Niedra. The Latvians eventually ousted the unpopular Niedra and restored their legitimate government, forcing out his German masters with Estonian and British help.
The experience of WWI and the early interwar years made the Baltic nations fear and resent the possibility of German occupation more than the possibility of Soviet occupation. Certainly the anti-Soviet feelings were not created by Stalin's repression; but this unexpected and extraordinary high level of repression is what made them stronger than the anti-German feelings...I don't see what would be so strange about that. For the record, I came across this assertion in War Land On The Eastern Front by Vejas Liulevicus (a Lithuanian-American historian whose family left their homeland to escape Soviet rule. So - putting it mildly - not a person likely to hold some kind of pro-Russian bias).
I understand that the people in the Baltic states were very divided on the matter of Germany and the USSR - in Estonia, for example, a slight majority of the people seems to have seen the Germans as a bigger threat, but then it seems that the majority of the political elite saw the USSR as the main threat. I base this estimate on the biography of the Estonian politician Jaan Tõnisson by Erkki Tuomioja. Perhaps we could say that from Lithuania and Latvia in the south to Estonia and Finland in the north, it was most likely for the people fear Germany in the south and the USSR in the north, due to simple historical and geographical reasons. The dichotomy between what the people believed and what the political establishment, being more in the know about actual foreign events and processes thought, is also important. By the 30s, things changed significantly from the early interwar years, and in Stalin's time a lot of horrible stories came out of the USSR. For those with more information about what actually happened east of the border, it would have been hard to realistically see Germany as the bigger threat, especially before the Nazis solidified their rule after the mid-30s.
For most people, the thing was, though, that they did not want to choose between the two nations and resented the possibility of being put to a position where a choice would be forced, wanting to be free and independent instead of becoming German or Soviet "allies" - people naturally knew that such an arrangement would mean subjugation and foreign domination by either of these major powers. The UK and France, or the Nordic nations, or even Poland would have been the nations most Baltic citizens would have chosen as nations to voluntarily ally with.
So, again (like hwyl also pointed out above), the Baltic peoples were not "relieved" to be occupied by the Soviets. True, a large part of the Baltic peoples seems to have been more afraid of German than Soviet occupation. But saying that they were "relieved" that Red Army troops and tanks rolled over their borders to end these nations' independence is like saying someone would be relieved being killed with an electric chair instead of being thrown to the lions. The end result, the death of national independence, was the same. The people did not need to see the Soviet repression of 40-41 to understand this.
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