One wonders whether the continued existence of independent Baltic states might have the unexpected major consequence of swaying Hitler's mind towards working with minorities.
I afraid only if one is obsessed with proving irrational dogma that leaving hostile territories next to your industrial heartland in a wake of struggle for survival was a really great idea for USSR's leadership. If anything, Stalin's annexion just heightened Baltics' willingness to work with Nazi. They became pre-fabricated just-add-water eager allies of Germans, begging Nazi leadership to let them collaborate. But even that eagernes did not lead Hitler toward pro-minority policy. What make you think that he would think otherwise if there's no invasion? Especially when he thought about Estonians and Latvians, who were German serfs fo 6-7 centuries. Work with governments of serfs, who started their regime with kicking their German barons out? Yeah, that's really really typical of Herr Hitler.
Key word "in 1941."
There was guerrilladom in the Baltics until the 1970s.
Guerilla had been dealt with before Stalin's death. Several crazy people who hid in woods on principle after that were more of local attraction, widely known secrets, and were tolerated as soon as they were non-violent. But as far as I understand we're talking about pre-1945, aren't we?
Furthermore, the hostile Baltic population provided a good recruiting ground for the Germans--IIRC there were entire SS divisions raised in the Baltics.
Balts' eagerness to serve Nazi has more complex explanation than Soviet brutality. After all, Soviets subjected Western Ukraine and Western Belarus to the same treatment in 1939-1940. Did they serve Nazi? Nosiree, they joined AK and OUN, nationalist movements that fought both Nazi and Reds (Edit - I should say that OUN was much more interesting in fighting Reds, but they still did not serve Germans with such unwavering eagerness). Germans were able to recruit single Ukrainian Waffen SS division (from 10 times more population) only after they made a lot of concessions to Ukrainians, including Orthodox priests, separate oath of allegiance and such.
Conquering Poland IIRC took around six weeks.
Polish government left Warsaw by Sep. 6 and Germans took every significant city and/or railroad station West of future Soviet-German border by Sep. 15 (couple of days before the Soviet invasion).
Furthermore, would the Baltics fall any faster than they did as Soviet-annexed provinces?
It took Germans 2 weeks to get through Poland. It took them two months to get through Red Army defending Baltic territories (Tallinn fell sometimes during last week of August). Well, that's pretty much answers your question, doesn't it?