Well the OTL Operation Osiovoakhim scientists would still be in Russia, working for the Soviet space program and rocketry, a patriotic thing for the Soviet Union, making their presence relatively acceptable.
Yes, but they're on a much lower scale (Say, hundreds) and largely kept from the public anyway for use on secret projects and such.
A few ten thousands of more skilled workers could be obtained in heavy industry and non-rocketry research and utilized in dispersed, localized numbers, largely for military purposes, which probably wouldn't be much of a problem either.
Well, a few thousand dispersed over the entirety RSFSR pretty much dilutes their effect from doing anything meaningful in the long term. I mean, you might get the occasional German who manages to make a breakthrough on a project, but the rest are going to be overwhelmingly constrained by the fact they're just one man in say an entire factory of hundreds if not thousands of workers. The social problems are also still going to be there, particular in terms of isolation and stigmatization.
The majority, an additional, almost 2 million German POWs without significant technical experience, could be settled in Central Asia and the Caucasus as a Sovietizing factor, working mostly in industry and agriculture. IOTL the Soviets settled Russians in Kazakhstan in the 50s and 60s, so there would be a perceived need to send settlers there.
I doubt they'd be settled in the Caucasus, due to the wartime connections between the Reich and resistance movements in the region. Dumping all those Germans in Central Asia also will breed issues, as the culture between the Germans and the natives is even more distinct.
On an interesting note, however, looking at Soviet mobilization data shows that by 1942, throughout the entirety of the Central Asia SSRs, there was only around 500,000 men fit for mobilization. Modern Turkmenistan, for example, as a whole only had ~1,200,000 people. Even splitting those 2 Million up five ways so that each SSR gets 500,000 men means that you're nearly going to entirely displace the native majorities with German culture (Assuming intermixing is able to occur on a large enough scale).